0000950170-25-034820 | 10-K | XBRL Viewer

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Net Loss per Share - Schedule of Potentially Common Shares Excluded from Calculation of Net Loss Per share (Detail) - shares	12 Months Ended
	Dec. 31, 2024	Dec. 31, 2023
Antidilutive Securities Excluded From Computation Of Earnings Per Share [Line Items]
Potentially Common Shares Excluded from Calculation of Net Loss Per share	7,913,412	8,062,921
Purchase Warrants
Antidilutive Securities Excluded From Computation Of Earnings Per Share [Line Items]
Potentially Common Shares Excluded from Calculation of Net Loss Per share	7,394,363	7,394,363
Unvested Restricted Common Stock Awards
Antidilutive Securities Excluded From Computation Of Earnings Per Share [Line Items]
Potentially Common Shares Excluded from Calculation of Net Loss Per share	194,066	36,046
Employee Stock Option
Antidilutive Securities Excluded From Computation Of Earnings Per Share [Line Items]
Potentially Common Shares Excluded from Calculation of Net Loss Per share	324,983	612,761
Potential Shares Issuable Under ESPP
Antidilutive Securities Excluded From Computation Of Earnings Per Share [Line Items]
Potentially Common Shares Excluded from Calculation of Net Loss Per share		19,751

Fair Value of Financial Instruments - Schedule of Assets measured at fair value and the gross unrealized holding gains and losses (Details) - USD ($) $ in Thousands	Dec. 31, 2024	Dec. 31, 2023
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Amortized Cost	$ 18,860	$ 23,958
Gross Unrealized Gain	0	2
Gross Unrealized Loss	0	0
Estimated Fair Value	18,860	23,960
Commercial paper \| Cash and cash equivalents
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Amortized Cost		8,482
Gross Unrealized Gain		2
Gross Unrealized Loss		0
Estimated Fair Value		8,484
Money market funds
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Amortized Cost	18,860	15,476
Gross Unrealized Gain	0	0
Gross Unrealized Loss	0	0
Estimated Fair Value	$ 18,860	$ 15,476

Fair Value of Financial Instruments - Schedule of Company's Classified Assets Measured at Fair Value on Recurring Basis (Detail) - USD ($) $ in Thousands	Dec. 31, 2024	Dec. 31, 2023
Assets:
Estimated Fair Value	$ 18,860	$ 23,960
Liabilities:
Purchase warrant laibility	4,874	21,047
Money market funds
Assets:
Estimated Fair Value	18,860	15,476
Commercial paper \| Cash and cash equivalents
Assets:
Estimated Fair Value		8,484
Recurring
Assets:
Total assets	18,860	47,746
Liabilities:
Purchase warrant laibility	4,874	21,047
Total liability	4,874	21,047
Recurring \| Money market funds
Assets:
Estimated Fair Value	18,860	15,476
Recurring \| Commercial paper
Assets:
Estimated Fair Value		14,342
Recurring \| Commercial paper \| Cash and cash equivalents
Assets:
Estimated Fair Value		8,484
Recurring \| U.S. Government Agency Securities and Treasuries
Assets:
Short-term investments		9,444
Recurring \| Quoted Prices in Active Markets for Identical Assets (Level 1)
Assets:
Total assets	18,860	22,432
Liabilities:
Purchase warrant laibility	0	0
Total liability	0	0
Recurring \| Quoted Prices in Active Markets for Identical Assets (Level 1) \| Money market funds
Assets:
Estimated Fair Value	18,860	15,476
Recurring \| Quoted Prices in Active Markets for Identical Assets (Level 1) \| Commercial paper
Assets:
Estimated Fair Value		0
Recurring \| Quoted Prices in Active Markets for Identical Assets (Level 1) \| Commercial paper \| Cash and cash equivalents
Assets:
Estimated Fair Value		0
Recurring \| Quoted Prices in Active Markets for Identical Assets (Level 1) \| U.S. Government Agency Securities and Treasuries
Assets:
Short-term investments		6,956
Recurring \| Significant Other Observable Inputs (Level 2)
Assets:
Total assets	0	25,314
Liabilities:
Purchase warrant laibility	0	0
Total liability	0	0
Recurring \| Significant Other Observable Inputs (Level 2) \| Money market funds
Assets:
Estimated Fair Value	0	0
Recurring \| Significant Other Observable Inputs (Level 2) \| Commercial paper
Assets:
Estimated Fair Value		14,342
Recurring \| Significant Other Observable Inputs (Level 2) \| Commercial paper \| Cash and cash equivalents
Assets:
Estimated Fair Value		8,484
Recurring \| Significant Other Observable Inputs (Level 2) \| U.S. Government Agency Securities and Treasuries
Assets:
Short-term investments		2,488
Recurring \| Significant Unobservable Inputs (Level 3)
Assets:
Total assets	0	0
Liabilities:
Purchase warrant laibility	4,874	21,047
Total liability	4,874	21,047
Recurring \| Significant Unobservable Inputs (Level 3) \| Money market funds
Assets:
Estimated Fair Value	$ 0	0
Recurring \| Significant Unobservable Inputs (Level 3) \| Commercial paper
Assets:
Estimated Fair Value		0
Recurring \| Significant Unobservable Inputs (Level 3) \| Commercial paper \| Cash and cash equivalents
Assets:
Estimated Fair Value		0
Recurring \| Significant Unobservable Inputs (Level 3) \| U.S. Government Agency Securities and Treasuries
Assets:
Short-term investments		$ 0

Available-for-Sale Securities

12 Months Ended

Dec. 31, 2024

Investments, Debt and Equity Securities [Abstract]

Available-for-Sale Securities

(4)

Available-for-Sale Securities

The following tables summarize the available-for-sale securities held at December 31, 2024 and 2023 (in thousands):



December 31, 2023	Amortized cost		Gross unrealized gains		Gross unrealized losses			Fair Value
Commercial paper	$	14,338	$	4	$	—		$	14,342
U.S. treasuries		9,444		1		(1	)		9,444
Total	$	23,782	$	5	$	(1	)	$	23,786

There were no available-for-sale securities held at December 31, 2024. The aggregate fair value of the securities in an unrealized loss position at December 31, 2023 was $5.4 million. The Company reviews its investments for other-than-temporary impairment whenever the fair value of an investment is less than amortized cost and evidence indicates that an investment’s carrying amount is not recoverable within a reasonable period of time. To determine whether an impairment is other-than-temporary, the Company considers whether it has the ability and intent to hold the investment until a market price recovery and considers whether evidence indicating the cost of the investment is recoverable outweighs evidence to the contrary. The Company did not hold any securities with an other-than-temporary impairment at December 31, 2024.

Gross realized gains and losses on the sales of investments have not been material to the Company’s consolidated statement of operations.

Consolidated Balance Sheets (Parenthetical) - $ / shares	Dec. 31, 2024	Dec. 31, 2023
Statement of Financial Position [Abstract]
Common stock, par value	$ 0.001	$ 0.001
Common stock, authorized	250,000,000	250,000,000
Common stock, Issued	11,975,901	9,465,949
Common stock, outstanding	11,696,109	9,186,157
Treasury stock, shares	279,792	279,792

Pay vs Performance Disclosure - USD ($) $ in Thousands	12 Months Ended
Pay vs Performance Disclosure - USD ($) $ in Thousands	Dec. 31, 2024	Dec. 31, 2023
Pay vs Performance Disclosure
Net Income (Loss)	$ (23,359)	$ (61,273)

- Definition

The portion of profit or loss for the period, net of income taxes, which is attributable to the parent.

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+ Details

Available-for-Sale Securities (Tables)

12 Months Ended

Dec. 31, 2024

Investments, Debt and Equity Securities [Abstract]

Summary of Available-for-Sale Securities Held

The following tables summarize the available-for-sale securities held at December 31, 2024 and 2023 (in thousands):



December 31, 2023	Amortized cost		Gross unrealized gains		Gross unrealized losses			Fair Value
Commercial paper	$	14,338	$	4	$	—		$	14,342
U.S. treasuries		9,444		1		(1	)		9,444
Total	$	23,782	$	5	$	(1	)	$	23,786

Leases - Components of Lease Cost for Operating Leases (Detail) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2024	Dec. 31, 2023
Operating leases
Operating lease cost	$ 1,582	$ 4,869
Variable lease cost	1,091	1,583
Total lease cost	$ 2,673	$ 6,452

Collaboration Agreements

12 Months Ended

Dec. 31, 2024

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Collaboration Agreements

(11)

Collaboration Agreements

Roche Collaboration

In June 2021, the Company entered into a Pilot Collaboration and Option Agreement (the Roche Collaboration and Option Agreement) with F. Hoffmann-La Roche Ltd (Roche Basel) and Hoffmann-La Roche Inc. (Roche US, and together with Roche Basel, Roche). Under the terms of the Roche Collaboration and Option Agreement, the Company and Roche collaborated to research and pre-clinically develop Synthetic Biotics for addressing an undisclosed novel target for the treatment of inflammatory bowel disease (the Product Candidate).

Pursuant to the Roche Collaboration and Option Agreement, Roche agreed to pay the Company, an upfront, nonrefundable technology access fee of $1.0 million, which the Company received in July 2021. In addition, the Company was eligible to receive up to $5.0 million in milestone payments upon the achievement of certain success criteria. The Company achieved all of the milestone payments and Roche paid the Company $5.0 million from September 2021 through October 2023. Following the research period, Roche held an exclusive option right (the Option) to negotiate a definitive Collaboration and License Agreement (CLA) for further development and commercialization of the Product Candidate. The Roche Collaboration and Option Agreement concluded after the last milestone was achieved by the Company in October 2023. Subsequently, Roche did not exercise its exclusive option to enter into a licensing and collaboration agreement for further development and commercialization of the product candidate.

Pursuant to the Roche Collaboration and Option Agreement, during the term of such agreement, each party had granted to the other party a non-exclusive, non-transferrable, non-sublicensable, royalty-free right and license to certain intellectual property and know-how controlled by such party, solely as necessary for the party to perform its obligations under the Roche Collaboration and Option Agreement. The parties established a Joint Research Committee (JRC) to oversee and manage the execution of the underlying study plan for the Roche Collaboration and Option Agreement.

The Company assessed this arrangement in accordance with ASC 606, Revenue from Contracts with Customers, and concluded that the contract counterparty, Roche, is a customer. The Company identified the following material promises made by the Company to Roche at the outset of the arrangement: (1) a non-exclusive royalty-free research and development license; (2) research and development services for pre-clinical activities under the research plan; (3) implicit renewal options created by Roche’s decision not to terminate the contract; (4) the Company’s participation on the JRC; and (5) an exclusive right to negotiate a definitive CLA for further development and commercialization of the Product Candidate. The Company determined that the license and research and development activities were not distinct from one another, as the license has limited value without the performance of research and development activities. The Company’s participation on the JRC was determined to be quantitatively and qualitatively immaterial and therefore is excluded from performance obligations. As such, the Company determined that the promises associated with the license and research and development services should be combined into a single performance obligation.

The Company evaluated the milestone payments relating to the three phases of research as defined in the research plan and the option to negotiate and enter into the CLA, to determine whether they provide Roche with any material rights. The Company concluded that the option was not issued at a significant and incremental discount, and therefore do not provide material rights. As such, they were excluded as performance obligations at the outset of the arrangement.

Based on these assessments, the Company identified one performance obligation at the outset of the Roche Collaboration and Option Agreement, which consisted of: (1) the non-exclusive license and (2) the research and development activities.

At the outset of the arrangement, the transaction price included only the $1.0 million up-front consideration received and which was allocated to the single performance obligation. The milestone payments that were received were excluded from the transaction price until each respective milestone was achieved.

Revenue associated with performance obligations under the Roche Collaboration and Option Agreement was recognized as the research and development services were provided using an input method, according to the full-time equivalents incurred. The transfer of control occurs over time and, in management’s judgment, was the best measure of progress towards satisfying the performance obligation.

The Company recognized $0.01 million and $3.4 million for the years ended December 31, 2024 and 2023, respectively, as collaboration revenue in the Company’s consolidated statements of operations and comprehensive loss.

Ginkgo Collaboration

In 2017, the Company established a technology collaboration with Ginkgo. In June 2019, in connection with the issuance to Ginkgo of an aggregate of 422,718 shares of common stock and Pre-Funded Warrants to purchase an aggregate of 169,874 common stock (See Note 9, Stockholders' Equity), the Company expanded its collaboration and entered into an agreement with Ginkgo for the research and development of engineered microbial therapeutic products. Under the 2019 expanded agreement, the Company made a prepayment to Ginkgo of $30.0 million for its foundry services that will be provided to the Company over an initial term of five years, which could be extended for an additional three years, subject to the satisfaction of specified conditions. Upon the expiration of such initial term and, if applicable, an additional term, any portion of the prepayment that has not been used to purchase services from Ginkgo will be retained by Ginkgo. In February 2024, the Company and its board of directors decided to discontinue the Synpheny-3 trial and significantly reduce its workforce and have made the decision to evaluate strategic options for the Company. As a result of this decision, the Company would no longer be purchasing services from Ginkgo. During the year ended December 31, 2024, the remaining $5.2 million of prepaid expenses related to this collaboration that were historically recorded in prepaid expenses and other current assets and prepaid research and development, net of current portion on the consolidated balance sheet, were recorded as restructuring and other charges on the consolidated statements of operations and comprehensive loss.

Stockholders' Equity - Additional Information (Detail) - USD ($) $ / shares in Units, $ in Thousands			1 Months Ended		12 Months Ended
	Oct. 03, 2023	Sep. 27, 2023	Jul. 31, 2021	Jun. 30, 2019	Dec. 31, 2024	Dec. 31, 2023	Feb. 20, 2024
Class Of Stock [Line Items]
Fair Value Adjustment of Warrants					$ (16,173)	$ 7,652
Commissions and Offering Expenses Payable	$ 19,600
Common stock, par value		$ 0.001			$ 0.001	$ 0.001
Reverse Stock Split Approval Date		Sep. 21, 2023
Preferred Stock Par Value							$ 0.001
Reverse Stock Split Decsription		the Company effected a reverse stock split of its shares of common stock, pursuant to which every fifteen (15) shares of the its issued and outstanding common stock was automatically converted into one (1) issued and outstanding share of common stock without any change in the par value of $0.001 per share
Series A Preferred Stock [Member]
Class Of Stock [Line Items]
Shares Issued, Price Per Share							$ 12
October 2023 Financing [Member]
Class Of Stock [Line Items]
Fair Value Adjustment of Warrants					$ 16,200
Proceeds from Warrant Exercises					$ 4,900
The purchase warrants were recorded as a liability	$ 13,400
October 2023 Financing [Member] \| Maximum
Class Of Stock [Line Items]
Percentage Of Common Stock Ownership To Exercise Warrant	9.99%
October 2023 Financing [Member] \| Minimum
Class Of Stock [Line Items]
Percentage Of Common Stock Ownership To Exercise Warrant	4.99%
Common Stock [Member] \| Underwritten Public Offering [Member]
Class Of Stock [Line Items]
Sale of common stock, shares	3,921,928
Shares Issued, Price Per Share	$ 2.84
Warrant [Member] \| October 2023 Financing [Member]
Class Of Stock [Line Items]
Warrants exercised					2,920,126
Common Stock And Warrants [Member] \| Underwritten Public Offering [Member]
Class Of Stock [Line Items]
Warrants To Purchase Shares Of Common Stock	3,472,435
Sale of stock, price per share	$ 2.839
Common Stock And Warrants [Member] \| October 2023 Financing [Member] \| Underwritten Public Offering [Member]
Class Of Stock [Line Items]
Warrants To Purchase Shares Of Common Stock	7,394,363
Sale of stock, price per share	$ 3.408
Pre-Funded Warrants
Class Of Stock [Line Items]
Proceeds from Warrant Exercises					$ 2	$ 1
Pre-Funded Warrants \| Common Stock [Member]
Class Of Stock [Line Items]
Sale of common stock, shares						3,921,928
Ginkgo Bioworks, Inc.
Class Of Stock [Line Items]
Sale of stock, price per share				$ 135
Proceeds, net of issuance costs, from issuance of common stock and pre-funded warrants				$ 79,900
Proceeds from issuance of common stock, net of issuance costs				$ 57,000
Ginkgo Bioworks, Inc. \| Common Stock [Member]
Class Of Stock [Line Items]
Sale of common stock, shares				422,718
Ginkgo Bioworks, Inc. \| Pre-Funded Warrants
Class Of Stock [Line Items]
Warrants to purchase shares of common stock				169,874
Warrants exercise price per share				$ 135
Warrants exercise price per share paid at closing of offering				$ 134.85
Proceeds from sale of pre-funded warrants, net of issuance costs				$ 22,900
Warrants exercised					0
Ginkgo Bioworks, Inc. \| Pre-Funded Warrants \| Maximum
Class Of Stock [Line Items]
Warrants to purchase shares of common stock				169,874
Unbeneficial percentage of ownership after exercise of common stock outstanding effect to issuance				19.99%
Jefferies, LLC \| At The Market [Member]
Class Of Stock [Line Items]
Sale of common stock, shares					7,839
Proceeds from issuance of common stock, net of issuance costs			$ 50,000		$ 20

Fair Value of Financial Instruments (Tables)

12 Months Ended

Dec. 31, 2024

Fair Value Disclosures [Abstract]

Schedule of Company's Classified Assets Measured at Fair Value on Recurring Basis

At December 31, 2024 and 2023, the Company has classified assets and liabilities measured at fair value on a recurring basis as follows (in thousands):


	Fair Value Measurements at Reporting Date Using
	December 31,		Quoted Prices in Active Markets for Identical Assets		Significant Other Observable Inputs		Significant Unobservable Inputs
Description	2024		(Level 1)		(Level 2)		(Level 3)
Assets:
Money market funds	$	18,860	$	18,860	$	—	$	—
Total	$	18,860	$	18,860	$	—	$	—
Liabilities:
Purchase warrant liability	$	4,874	$	—	$	—	$	4,874
Total	$	4,874	$	—	$	—	$	4,874

	Fair Value Measurements at Reporting Date Using
	December 31,		Quoted Prices in Active Markets for Identical Assets		Significant Other Observable Inputs		Significant Unobservable Inputs
Description	2023		(Level 1)		(Level 2)		(Level 3)
Assets:
Money market funds	$	15,476	$	15,476	$	—	$	—
Commercial paper (included in cash and cash equivalents)		8,484		—		8,484		—
Commercial paper		14,342		—		14,342		—
U.S. government agency securities and treasuries		9,444		6,956		2,488		—
Total	$	47,746	$	22,432	$	25,314	$	—
Liabilities:
Purchase warrant liability	$	21,047	$	—	$	—	$	21,047
Total	$	21,047	$	—	$	—	$	21,047

Schedule of Fair Value Assets and Liabilities Measured Gross Unrealized Gains and Losses

The following tables summarize the estimated fair value of the assets presented within cash and cash equivalents measured at fair value and the gross unrealized holding gains and losses (in thousands):


December 31, 2024	Amortized Cost		Gross unrealized gains		Gross unrealized losses		Fair Value
Money market funds (included in cash and cash equivalents)	$	18,860	$	—	$	—	$	18,860
Total	$	18,860	$	—	$	—	$	18,860

December 31, 2023	Amortized Cost		Gross unrealized gains		Gross unrealized losses		Fair Value
Money market funds (included in cash and cash equivalents)	$	15,476	$	—	$	—	$	15,476
Commercial paper (included in cash and cash equivalents)		8,482		2		—		8,484
Total	$	23,958	$	2	$	—	$	23,960

Schedule of Assumptions Used in Determining Fair Value of Warrants

The assumptions used in the Black-Scholes option-pricing model for the purchase warrants on the consolidated balance sheets at December 31, 2024 and December 31, 2023 are included below:


	December 31, 2024			December 31, 2023
Expected Term	3.75 years			4.75 years
Weighted-average, risk free interest rate		4.3	%		3.9	%
Expected volatility		90.0	%		94.0	%
Dividend yield		—			—
Strike price	$	3.41		$	3.41
Stock price	$	1.40		$	3.85

Employee Benefits - Additional Information (Detail) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2024	Dec. 31, 2023	Dec. 31, 2021	Dec. 31, 2020
Retirement Benefits [Abstract]
Eligible employees to contribute to 401(k) plan			50.00%	50.00%
Employee contribution, percentage			6.00%	4.00%
Maximum matching contributions as a percentage of eligible compensation			3.00%	2.00%
Employee contribution	$ 90	$ 300

Fair Value of Financial Instruments - Schedule of Assumptions Used in Determining Fair Value of Warrants (Details) - Warrant - $ / shares	12 Months Ended
	Dec. 31, 2024	Dec. 31, 2023
Share-Based Compensation Arrangement by Share-Based Payment Award [Line Items]
Expected Term	3 years 9 months	4 years 9 months
Weighted-average, risk-free interest rate	4.30%	3.90%
Expected volatility	90.00%	94.00%
Dividend yield	0.00%	0.00%
Strike price	$ 3.41	$ 3.41
Stock price	$ 1.4	$ 3.85

- Definition

Line items represent financial concepts included in a table. These concepts are used to disclose reportable information associated with domain members defined in one or many axes to the table.

+ References

Reference 1: http://www.xbrl.org/2003/role/disclosureRef
-Topic 718
-SubTopic 10
-Name Accounting Standards Codification
-Section 35
-Paragraph 1D
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147480483/718-10-35-1D

Reference 2: http://www.xbrl.org/2003/role/disclosureRef
-Topic 718
-SubTopic 10
-Name Accounting Standards Codification
-Section 35
-Paragraph 3
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147480483/718-10-35-3

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-Topic 718
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-Name Accounting Standards Codification
-Section 50
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-Publisher FASB
-URI https://asc.fasb.org/1943274/2147480429/718-10-50-2

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-Topic 718
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-Name Accounting Standards Codification
-Section 50
-Paragraph 2
-Subparagraph (a)(2)
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-Name Accounting Standards Codification
-Section 50
-Paragraph 2
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Reference 6: http://www.xbrl.org/2003/role/disclosureRef
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Reference 9: http://www.xbrl.org/2003/role/disclosureRef
-Topic 718
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-Name Accounting Standards Codification
-Section 50
-Paragraph 2
-Subparagraph (c)(1)(iv)
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-URI https://asc.fasb.org/1943274/2147480429/718-10-50-2

Reference 10: http://www.xbrl.org/2003/role/disclosureRef
-Topic 718
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-Section 50
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-Subparagraph (c)(1)(iv)(01)
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Reference 18: http://www.xbrl.org/2003/role/disclosureRef
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Reference 19: http://www.xbrl.org/2003/role/disclosureRef
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Reference 24: http://www.xbrl.org/2003/role/disclosureRef
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Reference 25: http://www.xbrl.org/2003/role/disclosureRef
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Reference 26: http://www.xbrl.org/2003/role/disclosureRef
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Reference 27: http://www.xbrl.org/2003/role/disclosureRef
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Reference 28: http://www.xbrl.org/2003/role/disclosureRef
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+ Details

Income Taxes - Schedule of Temporary Differences Between Basis of Deferred Tax Assets and Liabilities (Detail) - USD ($)
$ in Thousands

Dec. 31, 2024

Dec. 31, 2023

Dec. 31, 2022

Deferred tax assets:

Net operating loss carryforwards

$ 102,145

$ 87,396

Tax credit carryforwards

10,931

10,401

Accrued expenses

132

Property and equipment

1,113

Lease liabilities

4,718

Equity compensation

2,191

3,270

Amortizable intangibles

984

1,100

Amortizable research expenditures

^[1]

17,958

20,202

Other

Gross deferred tax assets

134,433

128,361

Deferred tax liabilities:

Right of use assets

(3,306)

Gross deferred tax liabilities

(3,306)

Valuation allowance

(134,433)

(125,055)

$ (109,599)

Net deferred tax assets

$ 0

[1]

Under the Tax Cuts and Jobs Act (TCJA), research and experimental (R&D) expenditures are capitalized and amortized under section 174 for tax years beginning after December 31, 2021. These costs are amortized for tax purposes over 5 years since the R&D was performed in the U.S. The unamortized balance of these costs is presented as a deferred tax asset in the table above.

Equity-based Compensation and Equity Incentive Plans - Schedule of Stock Option Activity Under 2015 and 2017 Plan (Parenthetical) (Detail) - shares	Dec. 31, 2024	Dec. 31, 2023
Share Based Compensation Arrangement By Share Based Payment Award Options Outstanding Weighted Average Exercise Price And Additional Disclosures [Abstract]
Number of options in money	0	512,972

Assets Held for Sale, Property and Equipment- Additional Information (Detail) - USD ($) $ in Thousands	3 Months Ended	12 Months Ended
	Jun. 30, 2024	Dec. 31, 2024	Dec. 31, 2023
Property, Plant and Equipment [Abstract]
Depreciation expense		$ 347	$ 1,958
Impairment Charge		800
Gain on disposal of assset related to auction sale	$ 1,300	$ 1,200

Equity-based Compensation and Equity Incentive Plans - Schedule of Weighted Average Assumption Used Black-Scholes Option-pricing Model for Stock Options Issued to Employees and Non-employees (Detail) - Employees and Nonemployees - 2015 and 2017 Plan	12 Months Ended
	Dec. 31, 2024	Dec. 31, 2023
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Expected term	5 years 7 months 6 days	6 years 2 months 12 days
Weighted-average, risk-free interest rate	3.90%	3.70%
Expected volatility	92.00%	82.40%
Dividend yield	0.00%	0.00%

- Definition

Line items represent financial concepts included in a table. These concepts are used to disclose reportable information associated with domain members defined in one or many axes to the table.

+ References

+ Details

Summary of Significant Accounting Policies

12 Months Ended

Dec. 31, 2024

Accounting Policies [Abstract]

Summary of Significant Accounting Policies

(2)

Summary of Significant Accounting Policies

Basis of Presentation

The accompanying consolidated financial statements have been prepared in accordance with accounting principles generally accepted in the United States (U.S.) (U.S. GAAP or GAAP).

Principles of Consolidation

The accompanying consolidated financial statements include the accounts of Synlogic and its wholly owned subsidiaries. All intercompany accounts and transactions have been eliminated in consolidation.

Use of Estimates

The preparation of financial statements in accordance with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets, liabilities, revenues and expenses, and related disclosure of contingent assets and liabilities at the date of the consolidated financial statements and the reported amounts of expenses during the reporting period. On an on-going basis, the Company’s management evaluates its estimates, including those related to research and development accruals and prepaids, accrued expenses, contingencies, and investments. The Company bases its estimates on historical experience and on various other assumptions that are believed to be reasonable, the results of which form the basis for making judgments about the carrying values of assets and liabilities. Actual results could differ from those estimates. Changes in estimates are reflected in reported results in the period in which they become known.

Cash Equivalents

The Company considers all highly liquid investment instruments with a remaining maturity when purchased of three months or less to be cash equivalents. Investments qualifying as cash equivalents consist of money market funds, including money market funds held in a sweep account. Cash equivalents are stated at cost plus accrued interest, which approximates fair value. The amount of cash equivalents included in cash and cash equivalents was approximately $18.9 million and $24.0 million at December 31, 2024 and 2023, respectively.

Concentration of Credit Risk

Financial instruments that potentially subject the Company to concentrations of credit risk include amounts held as cash, cash equivalents, marketable securities and restricted cash. The Company uses high quality, accredited financial institutions to maintain its balances, and accordingly, such funds are subject to minimal credit risk. The Company has not experienced any losses in such accounts and management believes that the Company is not exposed to significant credit risk due to the financial position of the depository institutions in which those deposits are held. The Company has no financial instruments with off-balance sheet risk of loss.

Restricted Cash

The Company held restricted cash of approximately $0.05 million and $1.1 million at December 31, 2024 and 2023, respectively. Restricted cash for the year ended December 31, 2024 relates to a collateral deposit for the Company credit card. Restricted cash for the year ended December 31, 2023 related to a letter of credit to secure its lease at the 301 Binney Street facility, which was terminated in June 2024, in addition to the collateral credit card deposit. The Company has classified the deposits as long-term restricted cash on its balance sheet, in both periods.

The following table provides a reconciliation of cash, cash equivalents, and restricted cash reported within the statement of financial position that sum to the total of the same such amounts shown in the consolidated statements of cash flows (in thousands).


	December 31,		December 31,
	2024		2023
Cash and cash equivalents	$	18,860	$	23,960
Restricted cash		50		1,097
Total cash, cash equivalents, and restricted cash shown in the consolidated statement of cash flows	$	18,910	$	25,057

Fair Value

The Company is required to disclose information on all assets and liabilities reported at fair value that enables an assessment of the inputs used in determining the reported fair values. Accounting Standards Codification (ASC) Topic 820, Fair Value Measurements and Disclosures, establishes a fair value hierarchy for those instruments measured at fair value that distinguishes between assumptions based on market data (observable inputs) and the Company’s own assumptions (unobservable inputs). The hierarchy consists of three levels:

•

Level 1 – Utilize observable inputs such as quoted prices in active markets for identical assets or liabilities;

•

Level 2 – Utilize data points that are either directly or indirectly observable, such as quoted prices, interest rates and yield curves;

•

Level 3 – Utilize unobservable data points in which there is little or no market data, which require the Company to develop its own assumptions for the asset or liability.

The Company evaluates transfers between levels at the end of each reporting period. There were no transfers of assets or liabilities between Level 1, Level 2 or Level 3 during the years ended December 31, 2024 and 2023.

Available-for-Sale Securities

The Company classifies all of its investments as available-for-sale based upon its intent with regard to such investments. The Company classifies investments as short-term when their remaining contractual maturities are one year or less from the balance sheet date, and as long-term when the investment has a remaining contractual maturity of more than one year from the balance sheet date. Available-for-sale securities are carried at fair value, with the unrealized gains and losses reported in other comprehensive income (loss). The amortized cost of debt securities in this category is adjusted for amortization of premiums and accretion of discounts to maturity. Such amortization is included in interest and investment income. Realized gains and losses and declines in value judged to be other than temporary on available-for-sale securities, are included in interest and investment income.

The cost of securities sold is based on the specific identification method. Interest and dividends on securities classified as available-for-sale are included in interest and investment income. To determine whether an other-than-temporary impairment exists, the Company considers whether it has the ability and intent to hold the investment until a market price recovery, and whether evidence indicating the recoverability of the cost of the investment outweighs evidence to the contrary.

Property and Equipment

Property and equipment, including leasehold improvements, are recorded at cost and depreciated over their estimated useful lives using the straight‑line method. Repairs and maintenance costs are expensed as incurred, whereas major improvements are capitalized as additions to property and equipment.

Depreciation begins at the time the asset is placed in service. Depreciation is provided over the following estimated useful lives:


Asset classification		Useful life
Computer and office equipment		3 years
Furniture and fixtures		5 years
Laboratory equipment		5 years
Leasehold improvements		Lesser of useful life or remaining lease term

Impairment of Long‑Lived Assets

Long‑lived assets are reviewed for impairment whenever events or changes in circumstances indicate that the carrying amount of the asset may not be recoverable. When such events occur, the Company compares the carrying amounts of the assets to their undiscounted expected future cash flows. If this comparison indicates that there is impairment, the amount of impairment is calculated as the difference between the carrying value and fair value of the asset. As a result of the corporate restructuring, further discussed in Note 8, Restructuring and Other Charges, there were various impairment charges recorded during the year ended December 31, 2024.

Leases

The Company uses judgement to assess if an arrangement is a lease at contract inception. An arrangement is a lease if the contract involves the use of a distinct identified asset, the lessor does not have substantive substitution rights and the Company obtains control of the asset throughout the period by obtaining substantially all of the economic benefit of the asset and the right to direct the use of the asset. Leases classified as operating leases are included in operating lease right-of-use (ROU) assets, current operating lease liabilities and noncurrent operating lease liabilities in our consolidated balance sheets. Finance leases are included in property and equipment and finance lease obligations in our consolidated balance sheet.

ROU assets represent the right-to-use an underlying asset for the lease term and lease liabilities represent the obligation to make lease payments arising from the lease. ROU assets and lease liabilities are recognized at the lease commencement date based on the estimated present value of lease payments over the lease term. The Company utilizes its incremental borrowing rate to determine the present value of lease payments. The incremental borrowing rate is the rate incurred to borrow similar funds, on a collateralized basis, over a comparable term in a similar economic environment.

The Company has elected to account for the lease and non-lease components for leases as a single component for classes of all underlying assets and allocate all of the contract consideration to the lease component only. Lease cost for operating leases is recognized on a straight-line basis over the lease term and is included in operating expenses on the statements of operations and comprehensive loss. Variable lease payments are included in lease operating expenses.

The lease term includes options to extend the lease when it is reasonably certain that option will be exercised. Leases with a term of 12 months or less are not recorded on the Company’s consolidated balance sheets.

Research and Development Costs

Costs incurred in research and development are expensed as incurred. The Company defers and capitalizes nonrefundable advance payments made by the Company for research and development activities until the related goods are received or the related services are performed.

Research and development expenses are comprised of costs incurred in performing research and development activities, including salary and benefits, equity-based compensation expense, laboratory supplies and other direct expenses, facilities expenses, overhead expenses, contractual services and other outside expenses.

When third-party service providers’ billing terms do not coincide with the Company’s period-end, the Company is required to make estimates of its obligations to those third parties, including clinical trial costs, contractual services costs and costs for supply of its drug candidates, incurred in a given accounting period and record accruals at the end of the period. The Company bases its estimates on the completion status of the research and development programs and the associated estimate of unbilled costs.

Warrants

The Company accounts for issued warrants either as a liability or equity in accordance with ASC 480-10, Accounting for Certain Financial Instruments with Characteristics of both Liabilities and Equity (“ASC 480-10”) or ASC 815-40, Accounting for Derivative Financial Instruments Indexed to, and Potentially Settled in, a Company’s Own Stock (“ASC 815-40”). The assessment considers whether the warrants are freestanding financial instruments pursuant to ASC 480, meet the definition of a liability pursuant to ASC 480, and whether the warrants meet all of the requirements for equity classification under ASC 815, including whether the warrants are indexed to the company’s own stock and whether the warrant holders could potentially require “net cash settlement” in a circumstance outside of the company’s control, among other conditions for equity classification. This assessment, which requires the

use of professional judgment, is conducted at the time of warrant issuance and as of each subsequent quarterly period end date while the warrants are outstanding.

Warrants that are equity-classified instruments and recorded in additional paid-in capital at issuance are not subject to remeasurement. The purchase warrants issued in October 2023 are liability classified and recorded at fair value using the Black-Scholes option-pricing model at issuance, with any subsequent changes in fair value recognized in the consolidated statements of operations. The Company periodically evaluates changes in facts and circumstances that could impact the classification of warrants.

Revenue recognition

The Company was generating revenue through a collaboration and option agreement with Roche for the development and commercialization of product candidates. The Roche Collaboration and Option Agreement concluded after the last milestone was achieved by the Company in October 2023. Subsequently, Roche did not exercise its exclusive option to enter into a licensing and collaboration agreement for further development and commercialization of the product candidate.

The Company evaluates collaboration agreements with respect to FASB ASC Topic 808, Collaborative Arrangements, considering the nature and contractual terms of the arrangement and the nature of its business operations to determine the classification of the transactions. When the Company is an active participant in the activity and exposed to significant risks and rewards dependent on the commercial success of the collaboration, it will record its transactions on a gross basis in the consolidated financial statements and describe the rights and obligations under the collaborative arrangement in the notes to the consolidated financial statements.

Under ASC 606, an entity recognizes revenue when its customer obtains control of promised goods or services, in an amount that reflects the consideration which the entity expects to receive in exchange for those goods or services. To determine revenue recognition for arrangements that an entity determines are within the scope of ASC 606, the entity performs the following five-step analysis: (i) identify the contract(s) with a customer; (ii) identify the performance obligations in the contract; (iii) determine the transaction price; (iv) allocate the transaction price to the performance obligations in the contract; and (v) recognize revenue when (or as) the entity satisfies a performance obligation. The Company only applies the five-step analysis to contracts when it is probable that the entity will collect the consideration it is entitled to in exchange for the goods or services it transfers to the customer. At contract inception, once the contract is determined to be within the scope of ASC 606, the Company assesses the goods or services promised within each contract and determines those that are performance obligations and assesses whether each promised good or service is distinct. The Company then recognizes as revenue the amount of the transaction price that is allocated to the respective performance obligation when (or as) the performance obligation is satisfied.

The Company may enter into collaboration agreements for research and development services, under which the Company may license certain rights to its product candidates to third parties. The terms of these arrangements typically include payment to the Company of one or more of the following: non-refundable, upfront license fees; reimbursement of certain costs; customer option exercise fees; development, regulatory and commercial milestone payments; and royalties on net sales of licensed products. Variable consideration is constrained until it is deemed not be at significant risk of reversal.

In determining the appropriate amount of revenue to be recognized as it fulfills its obligations under each of its agreements for which the collaboration partner is also a customer, the Company performs the following steps: (i) identification of the promised goods or services in the contract; (ii) determination of whether the promised goods or services are performance obligations including whether they are distinct in the context of the contract; (iii) measurement of the transaction price, including the constraint on variable consideration; (iv) allocation of the transaction price to the performance obligations; and (v) recognition of revenue when (or as) the Company satisfies each performance obligation. As part of the accounting for these arrangements, the Company must use significant judgment to determine: a) the number of performance obligations based on the determination under step (ii) above; b) the transaction price under step (iii) above; and c) the contract term and pattern of satisfaction of the performance obligations under step (v) above. The Company uses significant judgment to determine whether milestones or other variable consideration, except for royalties, should be included in the transaction price as described further below. The transaction price is allocated to the goods and services the Company expects to provide. The Company uses estimates to determine the timing of satisfaction of performance obligations, which may include the use of full-time equivalent time as a measure of satisfaction of performance obligations.

Amounts received prior to satisfying the revenue recognition criteria are recorded as deferred revenue in the Company’s consolidated balance sheets. Amounts expected to be recognized as revenue within the 12 months following the balance sheet date are classified as current deferred revenue. Amounts not expected to be recognized as revenue within the 12 months following the balance sheet date are classified as deferred revenue, net of current portion.

Licenses of Intellectual Property

In assessing whether a promise or performance obligation is distinct from the other promises, we consider factors such as the research, manufacturing and commercialization capabilities of the customer and the availability of the associated expertise in the general marketplace. In addition, we consider whether the customer can benefit from a promise for its intended purpose without the receipt of the remaining promises, whether the value of the promise is dependent on the unsatisfied promise, whether there are other vendors that could provide the remaining promise, and whether it is separately identifiable from the remaining promise. For licenses that are combined with other promises, we utilize judgment to assess the nature of the combined performance obligation to determine whether the combined performance obligation is satisfied over time or at a point in time and, if over time, the appropriate method of measuring progress for purposes of recognizing revenue. We evaluate the measure of progress each reporting period and, if necessary, adjust the measure of performance and related revenue recognition.

Research and Development Services

If an arrangement is determined to contain a promise or obligation for us to perform research and development services, we must determine whether these services are distinct from the other promises in the arrangement. In assessing whether the services are distinct from the other promises, we consider the capabilities of the customer to perform these same services. In addition, we consider whether the customer can benefit from a promise for its intended purpose without the receipt of the remaining promise, whether the value of the promise is dependent on the unsatisfied promise, whether there are other vendors that could provide the remaining promise, and whether it is separately identifiable from the remaining promise. For research and development services that are combined with other promises, we utilize judgment to assess the nature of the combined performance obligation to determine whether the combined performance obligation is satisfied over time or at a point in time and, if over time, the appropriate method of measuring progress for purposes of recognizing revenue. The estimates we use to record revenue relating to the combined performance obligation on an over time basis, include input methods such as full-time equivalent time incurred compared to the full-time equivalent time expected to be incurred in the future to satisfy the performance obligation, which require management judgment. We evaluate the measure of progress each reporting period and, if necessary, adjust the measure of performance and related revenue recognition. With this method, we must estimate total inputs required to satisfy a performance obligation and measure efforts expended to date to determine revenue recognition. This estimate of remaining inputs is subjective, as the research is novel, and therefore efforts to be successful may be different than the estimated efforts at the balance sheet date.

Customer Options

If an arrangement is determined to contain customer options that allow the customer to acquire additional goods or services, the goods and services underlying the customer options are not considered to be performance obligations at the outset of the arrangement, as they are contingent upon option exercise. The Company evaluates the customer options for material rights, that is, the option to acquire additional goods or services for free or at a discount. If the customer options are determined to represent a material right, the material right is recognized as a separate performance obligation at the outset of the arrangement. The Company allocates the transaction price to material rights based on an alternative approach when the goods or services are both (i) similar to the original goods and services in the contract and (ii) provided in accordance with the terms of the original contract. Under this alternative, the Company allocates the total amount of consideration expected to be received from the customer to the total goods or services expected to be provided to the customer. Amounts allocated to a material right are not recognized as revenue until the option is exercised and the performance obligation is satisfied.

Milestone Payments

At the inception of each arrangement that includes milestone payments, the Company evaluates whether a significant reversal of cumulative revenue provided in conjunction with achieving the milestones is probable and estimates the amount to be included in the transaction price using the most likely amount method. If it is probable that a significant reversal of cumulative revenue would not occur, the associated milestone value is included in the transaction price. Milestone payments that are not within the control of the Company or the licensee, such as regulatory approvals, are not considered probable of being achieved until those approvals are received. For other milestones, the Company evaluates factors such as the scientific, clinical, regulatory, commercial, and other risks that must be overcome to achieve the particular milestone in making this assessment. There is considerable judgment involved in determining whether it is probable that a significant reversal of cumulative revenue would not occur. At the end of each subsequent

reporting period, the Company reevaluates the probability of achievement of all milestones subject to constraint and, if necessary, adjusts its estimate of the overall transaction price. Any such adjustments are recorded on a cumulative catch-up basis, which would affect revenues and earnings in the period of adjustment.

Royalties

For arrangements that include sales-based royalties, including milestone payments based on a level of sales, and the license is deemed to be the predominant item to which the royalties relate, the Company recognizes revenue at the later of (i) when the related sales occur, or (ii) when the performance obligation to which some or all of the royalty has been allocated has been satisfied (or partially satisfied). To date, the Company has not recognized any royalty revenue resulting from any of its licensing arrangements.

Contract Costs

The Company recognizes as an asset the incremental costs of obtaining a contract with a customer if the costs are expected to be recovered. As a practical expedient, the Company recognizes the incremental costs of obtaining a contract as an expense when incurred if the amortization period of the asset that we otherwise would have recognized is one year or less. To date, the Company has not incurred any incremental costs of obtaining a contract with a customer.

Equity‑Based Compensation

The Company measures equity-based compensation to employees, non-employees and directors based on the grant date fair value of the awards and recognizes the associated expense in the financial statements over the requisite service period of the award, which is generally the vesting period. The fair value of each option and purchase rights under the employee stock purchase plan (ESPP) is estimated on the date of grant using the Black‑Scholes option‑pricing model. Expected volatility for the Company’s common stock is determined based on an average of the historical volatility of the Company and the historical volatility of a peer‑group of similar public companies. The expected term of options granted to employees is calculated using the simplified method, which represents the average of the contractual term of the option and the weighted-average vesting period of the option. The expected term of purchase rights for the ESPP is based on the duration of an offering period. The assumed dividend yield is based upon the Company’s expectation of not paying dividends in the foreseeable future. The risk‑free interest rate is based upon the U.S. Treasury yield curve commensurate with the expected term at the time of grant or remeasurement. Forfeitures are recognized as they occur.

The Company classifies equity-based compensation expense in its consolidated statements of operations and comprehensive loss in the same manner in which the award recipient’s payroll costs are classified or in which the award recipients’ service payments are classified.

Income Taxes

The Company accounts for income taxes using the asset and liability method, which requires the recognition of deferred tax assets and liabilities for the expected future tax consequences of events that have been recognized in the financial statements or in the Company’s tax returns. Deferred taxes are determined based on the difference between the financial reporting and tax basis of assets and liabilities using enacted tax rates in effect in the years in which the differences are expected to reverse. Changes in deferred tax assets and liabilities are recorded in the provision for income taxes. The Company assesses the likelihood that its deferred tax assets will be recovered from future taxable income and, to the extent it believes based upon the weight of available evidence, that it is more likely than not that all or a portion of deferred tax assets will not be realized, a valuation allowance is established through a charge to income tax expense. Potential for recovery of deferred tax assets is evaluated by estimating the future taxable profits expected and considering prudent and feasible tax planning strategies.

Uncertain tax positions represent tax positions for which reserves have been established. The Company accounts for uncertainty in income taxes recognized in the consolidated financial statements by applying a two-step process to determine the amount of tax benefit to be recognized. First, the tax position must be evaluated to determine the likelihood that it will be sustained upon external examination by the taxing authorities. If the tax position is deemed more likely than not to be sustained, the tax position is then assessed to determine the amount of benefit to be recognized in the financial statements. The amount of the benefit that may be recognized is the largest amount that has a greater than 50% likelihood of being realized upon ultimate settlement. The provision for income taxes includes the effects of any resulting tax reserves, or unrecognized tax benefits, that are considered appropriate as well as the related net interest and penalties.

Net Loss Per Share

Basic net loss per share is computed using the weighted-average number of shares of common stock outstanding during the period. Diluted net loss per share is computed using the sum of the weighted-average number of shares of common stock outstanding during the period and if dilutive, the weighted-average number of potential shares of common stock, including unvested restricted common stock, outstanding stock options and potential shares issuable under the ESPP.

Segment Information

Operating segments are defined as components of an enterprise about which separate discrete financial information is available for evaluation by the chief operating decision maker, or decision-making group, in deciding how to allocate resources and in assessing performance. The Company operates in one operating segment: discovery and development of Synthetic Biotics. The Company’s principal executive officer, as chief operating decision maker, manages and allocates resources to the operations of the Company on a total company basis. Prior to the corporate restructuring, all of the Company’s equipment, leasehold improvements and other fixed assets were physically located within the United States, and all agreements with its partners were denominated in U.S. dollars, except where noted.

Treasury Stock

Treasury stock purchases are accounted for under the cost method whereby the entire cost of the acquired stock is recorded as treasury stock.

Recently Issued and Adopted Accounting Pronouncements

From time to time, new accounting pronouncements are issued by the Financial Accounting Standards Board (FASB) or other accounting standard setting bodies that the Company adopts as of the specified effective date. Unless otherwise discussed below, recently issued pronouncements that are or will be applicable to the Company did not have, or are not expected to have, a material impact on its present or future consolidated financial statements or disclosures.

In November 2023, the Financial Accounting Standards Board (“FASB”) issued ASU 2023-07, Segment Reporting (Topic 280): Improvements to Reportable Segment Disclosures (“ASU 2023-07”). ASU 2023-07 requires disclosure of incremental segment information on an annual and interim basis. The amendments also require companies with a single reportable segment to provide all disclosures required by this amendment and all existing segment disclosures in ASC 280, Segment Reporting. The amendments are effective for fiscal years beginning after December 15, 2023, and interim periods beginning after December 15, 2024. The Company adopted ASU 2023-07, effective December 31, 2024, in these consolidated financial statements. ASU 2023-07 only impacted the disclosures and did not impact the consolidated financial statements. See Note 18, Segment Information, for disclosures related to the adoption of ASU 2023-07.

Equity-based Compensation and Equity Incentive Plans - Schedule of Restricted Common Stock Activity (Detail) - Restricted Common Stock - $ / shares	12 Months Ended
	Dec. 31, 2024	Dec. 31, 2023
Beginning balance, Number of unvested shares/units	36,046
Granted	362,700	10,803
Vested	(10,800)
Forfeited	(193,880)
Ending balance, Number of unvested shares/units	194,066	36,046
Beginning balance, Unvested Grant date fair value	$ 25.24
Granted	4.44
Vested	25.96
Forfeited	5.58
Ending balance, Unvested Grant date fair value	$ 5.97	$ 25.24

Net Loss per Share

12 Months Ended

Dec. 31, 2024

Earnings Per Share [Abstract]

Net Loss per Share

(12)

Net Loss per Share

The following table sets forth the computation of basic and diluted net loss per share (in thousands, except for share and per share amounts):


	Years Ended December 31,
	2024			2023
Numerator:
Net loss	$	(23,359	)	$	(61,273	)
Denominator:
Weighted-average common shares outstanding - basic and diluted		12,196,209			6,502,279
Net loss per share - basic and diluted	$	(1.92	)	$	(9.42	)

The Company’s potentially dilutive shares, which include purchase warrants, outstanding stock options, unvested restricted common stock and potential shares issuable under the ESPP, are considered to be common share equivalents and are only included in the calculation of diluted net loss per share when their effect is dilutive.

The following potential common shares, presented based on amounts outstanding at each period end, were excluded from the calculation of the diluted net loss per share attributable to common stockholders for the period indicated because including them would have had an anti-dilutive effect.


	As of December 31,
	2024		2023
Purchase warrants		7,394,363		7,394,363
Unvested restricted common stock awards		194,066		36,046
Outstanding options to purchase common stock		324,983		612,761
Potential shares issuable under the ESPP		—		19,751
		7,913,412		8,062,921

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2024	Dec. 31, 2023
Cash flows from operating activities:
Net loss	$ (23,359)	$ (61,273)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation	347	1,958
Gain on disposal of property and equipment	(1,160)	(11)
Impairment loss on fixed assets	5,011	0
Impairment loss on ROU assets	9,571	0
Gain on lease termination	(3,271)	0
Impairment of prepaid research and development	5,219	0
Equity-based compensation expense	3,169	2,806
Change in fair value warrant liability	(16,173)	7,652
Transaction costs allocated to warrant liabilities	0	905
Accretion/amortization of investment securities	(242)	(818)
Reduction in carrying amount of operating lease right of use asset	948	3,337
Changes in operating assets and liabilities:
Prepaid expenses and other current assets	1,033	(8)
Prepaid research and development, net of current portion	1,906	1,475
Accounts payable and accrued expenses	(2,256)	(2,653)
Deferred revenue	0	(882)
Operating lease liabilities	(12,417)	(4,093)
Other assets	16	(9)
Net cash used in operating activities	(31,658)	(51,614)
Cash flows from investing activities:
Purchases of marketable securities	(1,477)	(27,931)
Proceeds from maturity of marketable securities	25,499	66,898
Purchases of property and equipment	(14)	(214)
Proceeds from the sale of property and equipment	1,331	16
Net cash provided by investing activities	25,339	38,769
Cash flows from financing activities:
Payments on finance lease obligations	(4)	(13)
Proceeds from employee stock purchases and exercise of stock options	152	124
Proceeds from issuance of common stock, pre-funded warrants and purchase warrants, net of issuance costs	0	19,583
Net cash provided by financing activities	172	20,944
Net (decrease) increase in cash, cash equivalents and restricted cash	(6,147)	8,099
Cash, cash equivalents and restricted cash at beginning of period	25,057	16,958
Cash, cash equivalents and restricted cash at end of period	18,910	25,057
Supplemental disclosure of non-cash investing activities:
Decrease in right-of-use asset and operating lease liabilities due to lease termination	1,626	0
Assets acquired under operating lease obligation	0	1,083
Property and equipment sales included in other current assets	2	0
Property and equipment purchases included in accounts payable and accrued expenses	0	29
Supplemental disclosure of non-cash financing activities:
Cash paid for income taxes	5	14
Cash paid for interest	0	1
Issuance costs included in accounts payable and accrued expenses	0	6
Pre-Funded Warrants
Cash flows from financing activities:
Proceeds from exercise of warrants	2	1
At-the-market Offering
Cash flows from financing activities:
Proceeds from issuance of common stock, net of issuance costs	$ 22	$ 1,249

Employee Benefits

12 Months Ended

Dec. 31, 2024

Retirement Benefits [Abstract]

Employee Benefits

The Company has a defined contribution 401(k) plan for eligible employees. Employees are eligible to participate in the plan beginning on their date of hire. Under the terms of the plan, employees may make voluntary contributions as a percentage of compensation. The Company started to match employee contributions effective January 1, 2019. The Company matched 50% of the employee contributions to the 401(k) plan up to a maximum of 4% of the participating employee’s eligible earnings, resulting in a maximum company match of 2% of the participating employee’s eligible earnings, and subject to certain additional statutory dollar limitations. In 2021, the Company increased the match to 50% of the employee contributions up to a maximum of 6% of the participating employee’s eligible earnings, resulting in a maximum company match of 3% of the participating employee’s eligible

earnings, and subject to certain additional statutory dollar limitations. For the years ended December 31, 2024 and 2023, the Company made $0.09 million and $0.3 million contributions to the plan, respectively.

Consolidated Statements of Stockholders' Equity - USD ($)	Total	Pre-Funded Warrants	At-the-market Offering	Common Stock $0.001 Par Value	Common Stock $0.001 Par Value Pre-Funded Warrants	Common Stock $0.001 Par Value At-the-market Offering	Additional Paid-in Capital	Additional Paid-in Capital Pre-Funded Warrants	Additional Paid-in Capital At-the-market Offering	Accumulated Other Comprehensive Income (Loss)	Accumulated Deficit	Treasury Stock
Balance at Dec. 31, 2022	$ 82,610,000			$ 5,000			$ 442,303,000			$ (161,000)	$ (357,019)	$ (2,518,000)
Balance (in Shares) at Dec. 31, 2022				4,728,874								(279,792)
Proceeds from issuance of common stock, net of issuance costs		$ 7,087,000	$ 1,249,000		$ 4,000			$ 7,083,000	$ 1,249,000
Proceeds from issuance of common stock, net of issuance costs, Shares					3,921,928	115,966
Exercise of options	1,000			$ 1,000
Exercise of options, shares				669,126
Issuance of restricted stock, shares				10,803
Issuance of common stock under employee stock purchase plan	124,000						124,000
Issuance of common stock under employee stock purchase plan, Shares				34,478
Cancellation of restricted stock				(15,119)
Reverse split: fractional share adjustment				(107)
Equity-based compensation expense	2,806,000						2,806,000
Unrealized gain (loss) on securities	167,000									167,000
Net Income (Loss)	(61,273,000)										(61,273,000)
Balance at Dec. 31, 2023	32,771,000			$ 10,000			453,565,000			6,000	(418,292,000)	$ (2,518,000)
Balance (in Shares) at Dec. 31, 2023				9,465,949								(279,792)
Proceeds from issuance of common stock, net of issuance costs			$ 22,000						$ 22,000
Proceeds from issuance of common stock, net of issuance costs, Shares						7,839
Exercise of options	152,000	$ 2,000			$ 2,000		152,000
Exercise of options, shares				82,293	2,251,000
Issuance of restricted stock, shares				362,700
Cancellation of restricted stock				(193,880)
Equity-based compensation expense	3,169,000						3,169,000
Unrealized gain (loss) on securities	(6,000)									$ (6,000)
Net Income (Loss)	(23,359,000)										(23,359,000)
Balance at Dec. 31, 2024	$ 12,751,000			$ 12,000			$ 456,908,000				$ (441,651,000)	$ (2,518,000)
Balance (in Shares) at Dec. 31, 2024				11,975,901								(279,792)

Restructuring and Other Charges

12 Months Ended

Dec. 31, 2024

Restructuring and Related Activities [Abstract]

Restructuring and Other Charges

(8)

Restructuring and Other Charges

In February 2024, the Company and its board of directors decided to discontinue the Synpheny-3 trial and as a result are currently evaluating strategic options for the Company with a goal to enhance stockholder value, including the possibility of a merger or sale of the Company. Due to this decision there has been an interim evaluation of impairment of long-lived and other assets which is described in detail below.

The Company also announced a corporate restructuring that included a reduction in its workforce, leaving one remaining full-time employee, in addition to consultants, to, among other things, support the strategic review process and current business operations. In connection with the corporate restructuring, the Company recorded restructuring charges for severance and related costs of

$6.2 million during the year ended December 31, 2024, respectively. The Company also executed consulting agreements with a select number of former employees in which their equity continues to vest under the terms of the original award. The consulting services were determined to be non-substantive and as a result, the Company has accelerated the related stock compensation expense and recorded an additional $2.4 million to stock compensation included in restructuring charges for the year ended December 31, 2024.

In connection with the corporate restructuring, during the year ended December 31, 2024, restructuring and other charges also include impairment of the right-of-use assets associated with the Company's existing leased spaces of $9.6 million. On June 26, 2024 (the “Termination Date”), the Company entered into a Lease Termination Agreement (the “Termination Agreement”) for its corporate headquarters in Cambridge, Massachusetts, with the landlord which, effective immediately, terminated the lease. In exchange for the early termination of the lease pursuant to the Termination Agreement, the Company made a total termination payment of $10.6 million, of which $1.0 million was from a letter of credit associated with the lease and classified in the consolidated balance sheets as noncurrent restricted cash at December 31, 2023. As a result of the lease termination, the Company recorded a gain on lease termination, associated with its former headquarters, of $3.2 million, for the year ended December 31, 2024.

Impairment losses of $5.0 million, related to property and equipment primarily related to leasehold improvements in connection with the lease impairment were recorded for the year ended December 31, 2024. These charges have been offset by gains on equipment sales of $1.2 million for the year ended December 31, 2024.

Other charges relating to the restructuring include a $5.2 million charge to impairment for prepaid research and development in relation to the Ginkgo collaboration (See Note 11, Collaboration Agreements: Ginkgo Collaboration) for the year ended December 31, 2024. Additionally, there were charges of $1.2 million recorded during the year ended December 31, 2024, respectively related to the restructuring including legal fees, banking fees and lab decommissioning fees.

As of December 31, 2024, approximately $1.7 million of the total restructuring charges remain unpaid and were included in accrued restructuring charges. These charges primarily consist of personnel costs related to severance expense and retention bonuses, in addition to professional services costs.

Stockholders' Equity - Schedule of Shares of Common Stock Reserved for Future Issuance (Detail)	Dec. 31, 2024 shares
Class Of Stock [Line Items]
Total Shares of Common Stock Reserved for Future Issuance	8,347,906
Options Exercisable to Purchase Common Stock
Class Of Stock [Line Items]
Total Shares of Common Stock Reserved for Future Issuance	231,360
Common Stock Issuable Under Pre-Funded Warrants
Class Of Stock [Line Items]
Total Shares of Common Stock Reserved for Future Issuance	552,309
Common Stock Issuable Under Pre-Funded Warrants \| Ginkgo Bioworks Inc [Member]
Class Of Stock [Line Items]
Total Shares of Common Stock Reserved for Future Issuance	169,874
Purchase Warrants
Class Of Stock [Line Items]
Total Shares of Common Stock Reserved for Future Issuance	7,394,363

- Definition

Line items represent financial concepts included in a table. These concepts are used to disclose reportable information associated with domain members defined in one or many axes to the table.

+ References

Reference 1: http://www.xbrl.org/2003/role/exampleRef
-Topic 505
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-Name Accounting Standards Codification
-Section 50
-Paragraph 13
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Reference 2: http://www.xbrl.org/2003/role/recommendedDisclosureRef
-Topic 272
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Reference 3: http://www.xbrl.org/2003/role/disclosureRef
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Reference 4: http://www.xbrl.org/2009/role/commonPracticeRef
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Reference 5: http://www.xbrl.org/2003/role/disclosureRef
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Reference 6: http://www.xbrl.org/2003/role/disclosureRef
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Reference 7: http://www.xbrl.org/2003/role/disclosureRef
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Reference 8: http://www.xbrl.org/2003/role/disclosureRef
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Reference 9: http://www.xbrl.org/2003/role/disclosureRef
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-URI https://asc.fasb.org/1943274/2147481112/505-10-50-14

Reference 10: http://www.xbrl.org/2003/role/disclosureRef
-Topic 505
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-Paragraph 18
-Subparagraph (c)
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-URI https://asc.fasb.org/1943274/2147481112/505-10-50-18

Reference 11: http://www.xbrl.org/2003/role/disclosureRef
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Reference 12: http://www.xbrl.org/2003/role/disclosureRef
-Topic 210
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-Topic 505
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Reference 14: http://www.xbrl.org/2003/role/disclosureRef
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Reference 15: http://www.xbrl.org/2003/role/disclosureRef
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Reference 16: http://www.xbrl.org/2003/role/disclosureRef
-Topic 946
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-Paragraph 3
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-Publisher FASB
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Reference 17: http://www.xbrl.org/2003/role/disclosureRef
-Topic 946
-SubTopic 10
-Name Accounting Standards Codification
-Section S99
-Paragraph 3
-Subparagraph (SX 210.6-03(i)(2)(i))
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-URI https://asc.fasb.org/1943274/2147479886/946-10-S99-3

Reference 18: http://www.xbrl.org/2003/role/disclosureRef
-Topic 946
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-Name Accounting Standards Codification
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-Publisher FASB
-URI https://asc.fasb.org/1943274/2147479886/946-10-S99-3

+ Details

Equity-based Compensation and Equity Incentive Plans - Schedule of Equity-based Compensation Expenses (Detail) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2024	Dec. 31, 2023
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Equity-based compensation expense	$ 3,169	$ 2,806
Research and Development Expense
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Equity-based compensation expense	232	1,024
General and Administrative Expense
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Equity-based compensation expense	570	1,782
Restructuring charges: expense acceleration
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Equity-based compensation expense	$ 2,367	$ 0

Summary of Significant Accounting Policies - Schedule of Reconciliation of Cash, Cash Equivalents, and Restricted Cash (Detail) - USD ($) $ in Thousands	Dec. 31, 2024	Dec. 31, 2023	Dec. 31, 2022
Accounting Policies [Abstract]
Cash and cash equivalents	$ 18,860	$ 23,960
Restricted cash	50	1,097
Total cash, cash equivalents, and restricted cash shown in the consolidated statement of cash flows	$ 18,910	$ 25,057	$ 16,958

Collaboration Agreements - Additional Information (Detail) - USD ($) $ in Thousands	1 Months Ended		12 Months Ended
	Oct. 31, 2023	Jun. 30, 2019	Dec. 31, 2024	Dec. 31, 2023	Jun. 30, 2021
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Recognition of revenue			$ 8	$ 3,371
Common Stock \| Pre-Funded Warrants
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Sale of common stock, shares				3,921,928
Ginkgo Collaboration
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Non-current pre-paid research and development			5,200
Prepayment to related party for collaboration agreement		$ 30,000
Related party transaction collaboration agreement, initial term		5 years
Ginkgo Collaboration \| Pre-Funded Warrants
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Warrants to purchase shares of common stock		169,874
Ginkgo Collaboration \| Common Stock
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Sale of common stock, shares		422,718
Maximum \| Ginkgo Collaboration \| Pre-Funded Warrants
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Warrants to purchase shares of common stock		169,874
Roche Collaboration and Option Agreement
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Upfront, nonrefundable technology access fee					$ 1,000
Milestones payment upon achievement of certain success criteria					5,000
Upfront payments					$ 1,000
Milestone payments	$ 5,000
Recognition of revenue			$ 10	$ 3,400

Summary of Significant Accounting Policies - Schedule of Useful Life of Property and Equipment (Detail)	Dec. 31, 2024
Computer and Office Equipment
Property Plant And Equipment [Line Items]
Useful life	3 years
Furniture and Fixtures
Property Plant And Equipment [Line Items]
Useful life	5 years
Laboratory Equipment
Property Plant And Equipment [Line Items]
Useful life	5 years
Leasehold Improvements
Property Plant And Equipment [Line Items]
Property, Plant, and Equipment, Useful Life, Term, Description [Extensible Enumeration]	us-gaap:UsefulLifeTermOfLeaseMember

Document and Entity Information - USD ($) $ in Millions	12 Months Ended
Document and Entity Information - USD ($) $ in Millions	Dec. 31, 2024	Feb. 27, 2025	Jun. 28, 2024
Document Information [Line Items]
Document Type	10-K
Amendment Flag	false
Document Period End Date	Dec. 31, 2024
Document Fiscal Year Focus	2024
Document Fiscal Period Focus	FY
Entity Registrant Name	SYNLOGIC, INC.
Entity Central Index Key	0001527599
Current Fiscal Year End Date	--12-31
Entity Well-known Seasoned Issuer	No
Entity Current Reporting Status	Yes
Entity Voluntary Filers	No
Entity Filer Category	Non-accelerated Filer
Entity Small Business	true
Entity Emerging Growth Company	false
ICFR Auditor Attestation Flag	false
Document Financial Statement Error Correction [Flag]	true
Document Financial Statement Restatement Recovery Analysis [Flag]	true
Entity Shell Company	false
Entity Common Stock, Shares Outstanding		11,696,109
Entity Public Float			$ 4.1
Entity File Number	001-37566
Entity Incorporation, State or Country Code	DE
Entity Tax Identification Number	26-1824804
Entity Interactive Data Current	Yes
Entity Address, Address Line One	PO Box
Entity Address, Address Line Two	30
Entity Address, City or Town	Winchester
Entity Address, State or Province	MA
Entity Address, Postal Zip Code	01890
City Area Code	617
Local Phone Number	659-2802
Document Annual Report	true
Document Transition Report	false
Auditor Firm ID	185
Auditor Name	KPMG LLP
Auditor Location	Boston, Massachusetts, U.S.
Auditor Opinion	Opinion on the Consolidated Financial Statements We have audited the accompanying consolidated balance sheets of Synlogic, Inc. and subsidiaries (the Company) as of December 31, 2024 and 2023, the related consolidated statements of operations and comprehensive loss, stockholders’ equity, and cash flows for the years then ended and the related notes (collectively, the consolidated financial statements). In our opinion, the consolidated financial statements present fairly, in all material respects, the financial position of the Company as of December 31, 2024 and 2023, and the results of its operations and its cash flows for the years then ended, in conformity with U.S. generally accepted accounting principles.
Documents Incorporated by Reference	DOCUMENTS INCORPORATED BY REFERENCE The following documents (or parts thereof) are incorporated by reference into the following parts of this Form 10-K: Certain information required in Part III of this Annual Report on Form 10-K is incorporated from the registrant’s definitive proxy statement for the 2025 annual meeting of stockholders to be filed pursuant to Regulation 14A with the U.S. Securities and Exchange Commission within 120 days of the registrant’s fiscal year ended December 31, 2024.
Common Stock [Member]
Document Information [Line Items]
Trading Symbol	SYBX
Title of 12(b) Security	Common Stock, par value $0.001 per share
Security Exchange Name	NASDAQ
Preferred Stock [Member]
Document Information [Line Items]
Title of 12(b) Security	Preferred Stock Purchase Rights
Security Exchange Name	NASDAQ

Commitments and Contingencies	12 Months Ended
Commitments and Contingencies	Dec. 31, 2024
Commitments and Contingencies Disclosure [Abstract]
Commitments and Contingencies	Commitments and Contingencies In the ordinary course of business, the Company may be subject to legal proceedings, claims and litigation as the Company operates in an industry susceptible to patent legal claims. The Company accounts for estimated losses with respect to legal proceedings and claims when such losses are probable and estimable. Legal costs associated with these matters are expensed when incurred. The Company is not currently a party to any material legal proceedings.

Leases (Tables)

12 Months Ended

Dec. 31, 2024

Leases [Abstract]

Components of Lease Cost for Operating Leases

The components of lease cost for operating leases for the years ended December 31, 2024 and 2023 were (in thousands):


	For the years ended December 31,
Operating leases	2024		2023
Operating lease cost	$	1,582	$	4,869
Variable lease cost		1,091		1,583
Total lease cost	$	2,673	$	6,452

Equity-based Compensation and Equity Incentive Plans - Additional Information (Detail) - USD ($) $ / shares in Units, $ in Thousands			12 Months Ended
	Jan. 01, 2024	Nov. 09, 2023	Dec. 31, 2024	Dec. 31, 2023	Dec. 31, 2019
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Employee Benefits and Share-Based Compensation			$ 200
Weighted average grant date fair value per share of options granted to employees			$ 3.15	$ 6.07
Total fair value of awards vested			$ 1,300	$ 2,500
Employee unrecognized compensation expense			$ 100
Employee unrecognized compensation cost, period of recognition			1 year 6 months 21 days
Common stock, outstanding		539,685	11,696,109	9,186,157
Exercise price		$ 1.85
Incremental equity-based compensation expense				$ 200
Equity-based compensation expense			$ 3,169	2,806
Restricted Common Stock
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total fair value of awards vested			300	$ 400
Employee unrecognized compensation expense			$ 50
Employee unrecognized compensation cost, period of recognition			1 year 2 months 12 days
Granted			362,700	10,803
Equity-based compensation expense			$ 1,127	$ 362
Common Stock
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Issuance of common stock under employee stock purchase plan, Shares				34,478
Employee Stock
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Increase in number of shares available for issuance (in shares)	91,861
Percentage of discount for employees under ESPP			15.00%
Purchase price as a percentage of fair value under ESPP			85.00%
Equity-based compensation expense			$ (22)	$ 90
ESPP
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares available for future grants			186,995
Equity-based compensation expense			$ (20)	$ 100
Plan 2015
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Percentage of shares outstanding					5.00%
Increase in number of shares available for issuance (in shares)	459,307
2017 Plan and 2015 Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares available for future grants			714,497
2023 Inducement Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares available for future grants			50,000

Available-for-Sale Securities - Additional Information (Detail) $ in Millions	Dec. 31, 2024 Security	Dec. 31, 2023 USD ($)
Investments, Debt and Equity Securities [Abstract]
Aggregate fair value of securities in unrealized loss position \| $		$ 5.4
Number of securities with other than temporary impairment \| Security	0

Summary of Significant Accounting Policies (Tables)

12 Months Ended

Dec. 31, 2024

Accounting Policies [Abstract]

Schedule of Reconciliation of Cash, Cash Equivalents, and Restricted Cash


	December 31,		December 31,
	2024		2023
Cash and cash equivalents	$	18,860	$	23,960
Restricted cash		50		1,097
Total cash, cash equivalents, and restricted cash shown in the consolidated statement of cash flows	$	18,910	$	25,057

Schedule of Useful Life of Property and Equipment

Depreciation begins at the time the asset is placed in service. Depreciation is provided over the following estimated useful lives:


Asset classification		Useful life
Computer and office equipment		3 years
Furniture and fixtures		5 years
Laboratory equipment		5 years
Leasehold improvements		Lesser of useful life or remaining lease term

Stockholders' Equity (Tables)

12 Months Ended

Dec. 31, 2024

Equity [Abstract]

Schedule of Shares of Common Stock Reserved for Future Issuance

The Company has reserved for future issuance the following shares of common stock related to the potential exercise of warrants, exercise of stock options, and the employee stock purchase plan:


	December 31, 2024
Common stock issuable under pre-funded warrants		552,309
Common stock issuable under purchase warrants		7,394,363
Common stock issuable under Ginkgo pre-funded warrants		169,874
Options exercisable to purchase common stock		231,360
Total		8,347,906

Insider Trading Arrangements	3 Months Ended
Insider Trading Arrangements	Dec. 31, 2024
Trading Arrangements, by Individual
Rule 10b5-1 Arrangement Adopted	false
Non-Rule 10b5-1 Arrangement Adopted	false
Rule 10b5-1 Arrangement Terminated	false
Non-Rule 10b5-1 Arrangement Terminated	false
Rule 10b51 Arr Modified Flag	false
Non Rule 10b51 Arr Modified Flag	false

Prepaid Expenses and Other Current Assets (Tables)

12 Months Ended

Dec. 31, 2024

Text Block [Abstract]

Schedule of Prepaid Expenses and Other Current Assets

Prepaid expenses and other current assets consist of the following (in thousands):


	December 31,		December 31,
	2024		2023
Prepaid insurance	$	517	$	691
Prepaid research and development		128		788
Other prepaid expenses		110		536
Other current assets		75		146
Total prepaid expenses and other current assets	$	830	$	2,161

Stockholders' Equity

12 Months Ended

Dec. 31, 2024

Equity [Abstract]

Stockholders' Equity

(9)

Stockholders' Equity

Rights Plan

On February 20, 2024, the Board of Directors of the Company declared a dividend of one preferred share purchase right (a “Right”), payable on March 1, 2024, for each share of common stock of the Company outstanding on March 1, 2024 to the stockholders of record on that date and for certain warrants to purchase Common Stock outstanding on March 1, 2024. In connection with the distribution of the Rights, the Company entered into a Rights Agreement, dated as of February 20, 2024, between the Company and Equiniti Trust Company LLC, as rights agent (the "Rights Agreement").

Each Right entitles the registered holder to purchase from the Company one one-thousandth of a share of Series A Junior Participating Preferred Stock, par value $0.001 per share, of the Company (the “Series A Preferred Stock”) at a price of $12.00 per one one-thousandth of a share of Series A Preferred Stock represented by a Right (the “Purchase Price”), subject to adjustment.

The Rights were determined to have no value upon issuance and no rights were exercisable as of December 31, 2024.

Reverse Stock Split

On September 27, 2023, the Company effected a reverse stock split of its shares of common stock, pursuant to which every fifteen (15) shares of the its issued and outstanding common stock was automatically converted into one (1) issued and outstanding share of common stock without any change in the par value of $0.001 per share. The reverse stock split was approved by the stockholders on September 21, 2023 at a special meeting of stockholders.

October 2023 Financing

On October 3, 2023, the Company issued and sold, through an underwritten public offering:

•

3,921,928 shares of its common stock at a price of $2.84 per share less underwriting discounts and commissions;

•

pre-funded warrants to purchase up to 3,472,435 shares of its common stock at a price of $2.839 immediately following the consummation of the offering, and;

•

accompanying common stock warrants to purchase up to 7,394,363 shares of its common stock at a price of $3.408 per share exercisable immediately after issuance and expires five years from the date of issuance.

Each share of its common stock and each pre-funded warrant was sold together with a common warrant to purchase one share of its common stock. A holder of pre-funded warrants may not exercise the warrant if the holder, together with its affiliates, would beneficially own more than 4.99% (or, upon election by a holder prior to the issuance of any warrants, 9.99%) of the number of shares of common stock outstanding immediately after giving effect to such exercise. The net proceeds to the Company from the sale of common stock and pre-funded warrants through the offering, after deducting the underwriting discounts and commissions and offering expenses payable by the Company, were approximately $19.6 million.

The common stock and pre-funded warrants met the criteria for equity classification. The purchase warrants met the definition of a derivative instrument. Accordingly, upon issuance, the purchase warrants were recorded as a liability at fair value using the Black-Scholes option-pricing model in the amount of $13.4 million. Any subsequent changes in fair value of the purchase warrants is recognized in the consolidated statements of operations. The residual proceeds were allocated between the common stock and pre-funded warrants based on their relative fair values at the time of issuance. The amount allocated to the pre-funded warrants was recorded as a component of stockholders’ equity within additional paid-in capital.

At December 31, 2024, the fair value of the purchase warrants was $4.9 million. Accordingly, a gain on remeasurement of the purchase warrant liability of $16.2 million was recorded in the year ended December 31, 2024. Subsequent to their issuance and as of December 31, 2024, 2,920,126 pre-funded warrants have been exercised. None of the purchase warrants have been exercised since their issuance.

At-the-Market (ATM) Offering Program

In July 2021, the Company entered into a sales agreement with Jefferies, LLC (Jefferies) with respect to an ATM, under which the Company may offer and sell, from time to time at its sole discretion, shares of its common stock having aggregate sales proceeds of up to $50.0 million. Jefferies is not required to sell any specific amount but acts as the Company’s sales agent using commercially reasonable efforts consistent with its normal trading and sales practices. During the year ended December 31, 2024, 7,839 shares of common stock were sold pursuant to the sales agreement with Jefferies, resulting in net proceeds of approximately $0.02 million.

Ginkgo Warrants

In June 2019, the Company issued to Ginkgo Bioworks, Inc. (Ginkgo) 422,718 shares of common stock and accompanying Pre-Funded Warrants (the Pre-Funded Warrants) to purchase up to an aggregate of 169,874 shares of common stock, at a combined purchase price per share and Pre-Funded Warrant of $135. The Pre-Funded Warrants have an exercise price of $135 per share, with $134.85 of such exercise price paid at the closing of the offering. The proceeds, net of issuance costs, were approximately $79.9 million, $57.0 million related to the proceeds from sale of the common stock and $22.9 million related to the proceeds from sale of the Pre-Funded Warrants. The Pre-Funded Warrants may be exercised at any time until all of the Pre-Funded Warrants are exercised in full to the extent that, after giving effect to such issuance after exercise, Ginkgo would not beneficially own in excess of 19.99% of the number of shares of common stock outstanding immediately after giving effect to the issuance. The Pre-Funded Warrants were classified as a component of permanent equity and were recorded at the issuance date using a relative fair value allocation method. The Pre-Funded Warrants are equity classified because they are freestanding financial instruments that are legally detachable and separately exercisable from the equity instruments, are immediately exercisable, do not embody an obligation for the Company to repurchase its shares, and permit the holders to receive a fixed number of common shares upon exercise. In addition, such warrants do not provide any guarantee of value or return. In connection with the issuance to Ginkgo of common stock and Pre-Funded Warrants, the Company expanded its collaboration and entered into an agreement with Ginkgo for the research and development of engineered microbial therapeutic products. As a result of the Company's and its board of directors decision to discontinue the Synpheny-3 trial, the Company would no longer be purchasing services from Ginkgo. None of the Pre-Funded Warrants have been exercised as of December 31, 2024. (See Note 11, Collaboration Agreements: Ginkgo Collaboration).

The Company has reserved for future issuance the following shares of common stock related to the potential exercise of warrants, exercise of stock options, and the employee stock purchase plan:


	December 31, 2024
Common stock issuable under pre-funded warrants		552,309
Common stock issuable under purchase warrants		7,394,363
Common stock issuable under Ginkgo pre-funded warrants		169,874
Options exercisable to purchase common stock		231,360
Total		8,347,906

- Definition

The entire disclosure for equity.

+ References

Reference 1: http://www.xbrl.org/2003/role/disclosureRef
-Topic 505
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 13
-Subparagraph (b)
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147481112/505-10-50-13

Reference 2: http://www.xbrl.org/2003/role/disclosureRef
-Topic 505
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-URI https://asc.fasb.org/1943274/2147481112/505-10-50-13

Reference 3: http://www.xbrl.org/2003/role/disclosureRef
-Topic 505
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-URI https://asc.fasb.org/1943274/2147481112/505-10-50-14

Reference 4: http://www.xbrl.org/2003/role/disclosureRef
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-URI https://asc.fasb.org/1943274/2147477968/946-235-50-2

Reference 5: http://www.xbrl.org/2003/role/disclosureRef
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-URI https://asc.fasb.org/1943274/2147477968/946-235-50-2

Reference 6: http://www.xbrl.org/2003/role/disclosureRef
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-URI https://asc.fasb.org/1943274/2147478448/946-505-50-6

Reference 7: http://www.xbrl.org/2003/role/disclosureRef
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Reference 8: http://www.xbrl.org/2003/role/disclosureRef
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-URI https://asc.fasb.org/1943274/2147480008/505-10-S99-1

Reference 9: http://www.xbrl.org/2003/role/disclosureRef
-Topic 235
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-Paragraph 1
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-URI https://asc.fasb.org/1943274/2147480678/235-10-S99-1

Reference 10: http://fasb.org/us-gaap/role/ref/legacyRef
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-Name Accounting Standards Codification
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-URI https://asc.fasb.org/505/tableOfContent

Reference 11: http://www.xbrl.org/2003/role/disclosureRef
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Reference 12: http://www.xbrl.org/2003/role/disclosureRef
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-URI https://asc.fasb.org/1943274/2147481112/505-10-50-13

Reference 13: http://www.xbrl.org/2003/role/disclosureRef
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-URI https://asc.fasb.org/1943274/2147481112/505-10-50-13

Reference 14: http://www.xbrl.org/2003/role/disclosureRef
-Topic 505
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-Name Accounting Standards Codification
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-URI https://asc.fasb.org/1943274/2147481112/505-10-50-14

Reference 15: http://www.xbrl.org/2003/role/disclosureRef
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Reference 16: http://www.xbrl.org/2003/role/disclosureRef
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Reference 17: http://www.xbrl.org/2003/role/disclosureRef
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Reference 18: http://www.xbrl.org/2003/role/disclosureRef
-Topic 505
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-URI https://asc.fasb.org/1943274/2147481112/505-10-50-18

Reference 19: http://www.xbrl.org/2003/role/disclosureRef
-Topic 505
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-Subparagraph (d)
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147481112/505-10-50-18

+ Details

Equity-based Compensation and Equity Incentive Plans

12 Months Ended

Dec. 31, 2024

Share-Based Payment Arrangement [Abstract]

Equity-based Compensation and Equity Incentive Plans

(10)

Equity‑based Compensation and Equity Incentive Plans

Equity Plans

The Company currently has four active equity plans.

The 2015 Equity Incentive Award Plan (2015 Plan) functions as the primary equity plan for the Company. The 2015 Plan includes an “evergreen provision” that allows for an annual increase in the number of shares of common stock available for issuance under the 2015 Plan, which annual increase will be added on the first day of each fiscal year from 2016 through 2025, inclusive, and will be equal to the lesser of (i) five percent of the shares outstanding on the last day of the immediately preceding fiscal year and (ii) such smaller number of shares as determined by the Board of Directors. On January 1, 2024, the Company added 459,307 shares to the 2015 Plan pursuant to the “evergreen provision”. The 2015 Plan provides for the granting of a variety of stock‑based compensation awards, including stock options, stock appreciation rights, restricted stock awards, restricted stock unit awards, deferred stock awards, dividend equivalent awards, stock payment awards, performance awards and other stock‑based awards.

The 2017 Stock Incentive Plan (the 2017 Plan) provides for the grant of incentive stock options, non-qualified stock options, restricted and unrestricted stock awards and other stock-based awards.

The 2015 Employee Stock Purchase Plan (ESPP) allows eligible employees to purchase shares of the Company’s common stock at a discount through payroll deductions of up to 15% of their eligible compensation, subject to any plan limitations. The ESPP generally provides for set offering periods, and at the end of each offering period, employees are able to purchase shares at 85% of the lower of the fair market value of the Company’s common stock on the first trading day of the offering period or on the last trading day of the offering period. The Company suspended the ESPP in 2017. In December 2019, the Board reactivated the 2015 ESPP and approved an amendment to the ESPP to (i) reduce the permitted payroll deduction and number of shares of the Company’s common stock that a participant may purchase per calendar year and offering period under the ESPP and (ii) establish a period for enrollment for eligible participants. The reactivation of the 2015 ESPP was effective immediately. The Company’s executive officers are eligible to participate in the 2015 ESPP. The ESPP includes an “evergreen provision,” allowing for an annual increase in the number of shares of common stock available for issuance. On January 1, 2024, the Company added 91,861 shares to the ESPP pursuant to the “evergreen provision”. Due to the corporate restructuring, the purchases for the ESPP offering periods were cancelled during the year ended December 31, 2024.

The 2023 Inducement Equity Incentive Award Plan (the 2023 Inducement Plan) was established as of December 8, 2023 to provide for the granting of equity awards to individuals who were not previously employees of Synlogic, or following a bona fide period of non-employment, as an inducement material to such individuals’ entering into employment with Synlogic, pursuant to Nasdaq Listing Rule 5635(c)(4). No shares were issued under the 2023 Inducement Plan during the year ended December 31, 2024.

As of December 31, 2024, there were an aggregate of 714,497 shares available for future grant under the 2015 Plan and the 2017 Plan, 186,995 shares available for future grant under the ESPP, and 50,000 shares available for future grant under the 2023 Inducement Plan.

Stock Options

The weighted average assumptions used in the Black-Scholes option-pricing model for stock options issued to employees and non-employees under the 2015 Plan and the 2017 Plan, during the years ended December 31, 2024 and 2023 were:


	Years Ended December 31,
Employees:	2024	2023
Expected term	5.6 years	6.2 years
Weighted-average, risk-free interest rate	3.9%	3.7%
Expected volatility	92.0%	82.4%
Dividend yield	—	—

The following table summarizes stock option activity under the 2015 and 2017 Plans.


	Stock options outstanding
						Weighted
						average
				Weighted		remaining		Aggregate
				average		contractual		intrinsic
	Number of			exercise		term		value (a)
	options			price		(in years)		(in thousands)
Outstanding at December 31, 2023		612,761		$	9.13		7.8	$	1,026
Granted		44,701			4.20				—
Exercised		(82,293	)		1.85				5
Cancelled/Forfeited		(250,186	)		7.08				—
Outstanding at December 31, 2024		324,983			11.88		7.0	$	—

Vested or expected to vest at December 31, 2024		324,983		$	11.88		7.0	$	—
Exercisable at December 31, 2024		231,360		$	15.94		6.7	$	—

(a) The aggregate intrinsic value is calculated as the difference between the exercise price of the options and the fair market value of the underlying common stock for the options that were in the money at December 31, 2024 and 2023. There were no options in the money at December 31, 2024. 512,972 options were in the money at December 31, 2023.

The weighted average grant date fair value per share of options granted during the years ended December 31, 2024 and 2023 was approximately $3.15 and $6.07, respectively. The total fair value of awards that vested during the years ended December 31, 2024 and 2023 was $1.3 million and $2.5 million, respectively.

As of December 31, 2024, there was approximately $0.1 million of unrecognized share-based compensation for unvested stock option grants which is expected to be recognized over a weighted average period of 1.56 years. The total unrecognized share-based compensation cost will be adjusted for actual forfeitures as they occur.

On November 9, 2023, the Company’s board of directors approved a stock option repricing, which repriced certain outstanding stock options held by then current employees. There were 539,685 outstanding eligible stock options that were amended to reduce such exercise price to $1.85 per share, the current fair market value of the Company’s common stock on the date of the approval of the repricing. Except for the modified exercise price, all other terms and conditions of each of the eligible stock options remained in full force and effect. The repricing was recorded as a stock option modification whereby the incremental fair value of each option was determined using the Black-Scholes option-pricing model at the date of the modification, and $0.2 million was recognized related to vested options as incremental equity-based compensation expense during the year ended December 31, 2023. The Company is recognizing the remaining $0.2 million of incremental equity-based compensation expense on a straight-line basis over the remaining requisite service period of the stock options.

Restricted Common Stock

During the years ended December 31, 2024 and 2023, 362,700 and 10,803 shares of restricted common stock were granted, respectively.

The following table shows restricted common stock activity:


	Restricted stock awards
				Weighted average grant date
	Number of			fair value
	shares			(per share)
Unvested at December 31, 2023		36,046		$	25.24
Granted		362,700			4.44
Vested		(10,800	)		25.96
Forfeited		(193,880	)		5.58
Unvested at December 31, 2024		194,066		$	5.97

The total fair value of shares that vested during the years ended December 31, 2024 and 2023 was $0.3 million and $0.4 million, respectively.

As of December 31, 2024, there was approximately $0.05 million of unrecognized share-based compensation related to restricted stock awards granted, which is expected to be recognized over a weighted average period of 1.2 years. The total unrecognized share-based compensation cost will be adjusted for actual forfeitures as they occur.

Employee Stock Purchase Plan

The ESPP is considered a compensatory plan with the related compensation expense recognized over the six-month offering periods. The compensation expense for the year ended December 31, 2024 was $(0.02) million due to the reversal of the expense as a result of the corporate restructuring and subsequent cancellation of the ESPP purchase in the first quarter of 2024. The compensation expense for the year ended December 31, 2023 was less than $0.1 million.

Equity Compensation

The Company has recorded total equity‑based compensation expense of approximately $3.2 million and $2.8 million, during the years ended December 31, 2024 and 2023, respectively. Equity compensation during the years ended December 31, 2024 and 2023 is derived from stock options, restricted stock awards, and the ESPP.

The following table summarizes equity‑based compensation expense within the Company’s consolidated statements of operations and comprehensive loss for the years ended December 31, 2024 and 2023 (in thousands):


	Years Ended December 31,
	2024		2023
Research and development	$	232	$	1,024
General and administrative		570		1,782
Restructuring charges: expense acceleration		2,367		—
	$	3,169	$	2,806

The following table summarizes equity‑based compensation expense by type of award for the years ended December 31, 2024 and 2023 (in thousands):


	Years Ended December 31,
	2024			2023
Stock options	$	2,064		$	2,354
Restricted stock awards		1,127			362
ESPP		(22	)		90
	$	3,169		$	2,806

Income Taxes - Schedule of Valuation Allowance - (Detail) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2024	Dec. 31, 2023
Income Tax Disclosure [Abstract]
Balance at beginning of year	$ (125,055)	$ (109,599)
Increase in valuation allowance	(9,378)	(15,456)
Balance at end of year	$ (134,433)	$ (125,055)

Income Taxes - Additional Information (Detail) - USD ($)	12 Months Ended
	Dec. 31, 2024	Dec. 31, 2023	Dec. 31, 2022
Income Tax Disclosure [Line Items]
Income tax expense	$ 5,000	$ 14,000
Valuation allowance	134,433,000	125,055,000	$ 109,599,000
Net operating loss carryforwards	$ 377,200,000
Description of tax benefit likely to be realized upon settlement	greater than 50%
Unrecognized tax benefits	$ 0
Interest or penalties accrued	$ 0	0
Income tax examination description	In the normal course of business, the Company is subject to examination by federal and state jurisdictions, where applicable. There are currently no pending tax examinations. Tax years from 2021 to the present are open to examination under the statute.
Maximum
Income Tax Disclosure [Line Items]
Income tax expense	$ 0	0
Federal
Income Tax Disclosure [Line Items]
Net operating loss carryforwards	377,200,000
Net operating loss carryforwards subject to expiration	62,400,000
Net operating loss carryforwards not subject to expiration	$ 314,800,000
Federal \| Minimum [Member]
Income Tax Disclosure [Line Items]
Net operating loss carryforwards expiration year	2034
Federal \| Maximum
Income Tax Disclosure [Line Items]
Net operating loss carryforwards expiration year	2037
State
Income Tax Disclosure [Line Items]
Net operating loss carryforwards		362,700,000
Net operating loss carryforwards expiration year	2029
State \| Research and Development.
Income Tax Disclosure [Line Items]
Tax credit carryforwards	$ 7,500,000	$ 4,400,000

Income Taxes - Reconciliation of Statutory Federal Income Tax Rate to Company's Effective Income Tax Rate (Detail)	12 Months Ended
	Dec. 31, 2024	Dec. 31, 2023
Income Tax Disclosure [Abstract]
U.S. federal statutory rate	21.00%	21.00%
State income taxes, net of federal benefit	9.00%	6.00%
Other permanent differences	9.00%	(3.00%)
Tax credits	2.00%	2.00%
Other items	(1.00%)	(1.00%)
Net change in valuation allowance	(40.00%)	(25.00%)
Effective income tax rate	0.00%	0.00%

Income Taxes

12 Months Ended

Dec. 31, 2024

Income Tax Disclosure [Abstract]

Income Taxes

(13)

Income Taxes

During the years ended December 31, 2024 and 2023, the Company recorded no income tax benefits for the net operating losses incurred due to its uncertainty of reclaiming a benefit for those losses.

Deferred taxes are recognized for temporary differences between the basis of assets and liabilities for financial statement and income tax purposes. Deferred tax assets consist of the following (in thousands):


	December 31,
	2024			2023
Deferred tax assets:
Net operating loss carryforwards	$	102,145		$	87,396
Tax credit carryforwards		10,931			10,401
Accrued expenses		132			84
Property and equipment		28			1,113
Lease liabilities		—			4,718
Equity compensation		2,191			3,270
Amortizable intangibles		984			1,100
Amortizable research expenditures (1)		17,958			20,202
Other		64			77
Gross deferred tax assets		134,433			128,361
Deferred tax liabilities:
Right of use assets		—			(3,306	)
Gross deferred tax liabilities		—			(3,306	)
Valuation allowance		(134,433	)		(125,055	)
Net deferred tax assets	$	—		$	—

(1) Under the Tax Cuts and Jobs Act (TCJA), research and experimental (R&D) expenditures are capitalized and amortized under section 174 for tax years beginning after December 31, 2021. These costs are amortized for tax purposes over 5 years since the R&D was performed in the U.S. The unamortized balance of these costs is presented as a deferred tax asset in the table above.

Management of the Company has evaluated the positive and negative evidence bearing upon the realizability of the Company’s deferred tax assets, which are comprised principally of net operating loss carryforwards, and determined that it is more likely than not that the Company will not recognize the benefits of the deferred tax assets. As a result, a full valuation allowance of approximately $134.4 million and $125.1 million was established at December 31, 2024 and 2023, respectively.

A reconciliation of the statutory federal income tax rate to the Company’s effective income tax rate is as follows:


	Years ended December 31,
	2024			2023
	Tax Rate			Tax Rate
U.S. federal statutory rate		21	%		21	%
State income taxes, net of federal benefit		9	%		6	%
Other permanent differences		9	%		(3	)%
Tax credits		2	%		2	%
Other items		(1	)%		(1	)%
Net change in valuation allowance		(40	)%		(25	)%
Effective income tax rate		—			—

Due to the previously disclosed purchase warrants error, as disclosed in Note 3 of the Quarterly report for the period ended September 30, 2024, the prior period reconciliation above was revised to reflect the impact of the error for the year ended December 31, 2023.

A roll-forward of the valuation allowance for the years ended December 31, 2024 and 2023 is as follows (in thousands):


	Years ended December 31,
	2024			2023
Balance at beginning of year	$	(125,055	)	$	(109,599	)
Increase in valuation allowance		(9,378	)		(15,456	)
Balance at end of year	$	(134,433	)	$	(125,055	)

As of December 31, 2024, the Company had federal net operating loss carryforwards that may be available to reduce future taxable income of $377.2 million. Of the $377.2 million of federal net operating loss carryforwards, $62.4 million will expire on various dates from 2034 to 2037. The remaining $314.8 million of federal net operating loss carryforwards do not expire. The Company also had state net operating loss carryforwards that may be available to reduce future taxable income of $362.7 million for the period ended December 31, 2024. The state net operating loss carryforwards begin to expire in 2029. In addition, as of December 31, 2024, the Company had federal and state research and development tax credit carryforwards available to reduce future tax liabilities of $7.5 million and $4.4 million, respectively.

Pursuant to Section 382 of the Internal Revenue Code of 1986 (IRC), certain substantial changes in the Company’s ownership may result in a limitation on the amount of net operating loss (NOL) carryforwards and research and development credit (R&D credit) carryforwards that may be used in future years. Utilization of the NOL and R&D credit carryforwards may be subject to a substantial annual limitation under Section 382 of the IRC due to ownership change limitations that have occurred previously or that could occur in the future. These ownership changes may limit the amount of NOL and R&D credit carryforwards that can be utilized annually to offset future taxable income and tax. The Company has not completed a study to assess whether an ownership change has occurred, or whether there have been multiple ownership changes since its formation, due to the significant complexity and related costs associated with such a study. There could be additional ownership changes in the future that may result in additional limitations on the utilization of NOL carryforwards and credits.

The Company is required to determine whether a tax position of the Company is more likely than not to be sustained upon examination, including resolution of any related appeals of litigation processes, based on the technical merits of the position. For tax positions meeting the more likely than not threshold, the tax amount recognized in the financial statements is reduced by the largest benefit that has a greater than fifty percent likelihood of being realized upon the ultimate settlement with the relevant taxing authority. The Company has not recognized any liability for unrecognized tax benefits as of December 31, 2024. The Company’s policy is to record interest and penalties related to unrecognized tax benefits on the income tax expense line in the consolidated statement of operations. There are no interest or penalties accrued at December 31, 2024 and 2023.

The Company files tax returns, on an entity-level basis, as prescribed by the tax laws of the jurisdictions in which it operates. In the normal course of business, the Company is subject to examination by federal and state jurisdictions, where applicable. There are currently no pending tax examinations. Tax years from 2021 to the present are open to examination under the statute. The Company’s net operating losses and other attributes generated in a closed tax year may still be adjusted to determine the amount of carryforward deduction available in an open year under examination.

- Definition

The entire disclosure for income tax.

+ References

Reference 1: http://www.xbrl.org/2003/role/disclosureRef
-Topic 740
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 12
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147482685/740-10-50-12

Reference 2: http://www.xbrl.org/2003/role/exampleRef
-Topic 740
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-Section 55
-Paragraph 231
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147482663/740-10-55-231

Reference 3: http://www.xbrl.org/2003/role/disclosureRef
-Topic 740
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Reference 4: http://www.xbrl.org/2003/role/disclosureRef
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Reference 6: http://www.xbrl.org/2003/role/disclosureRef
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Reference 10: http://www.xbrl.org/2003/role/disclosureRef
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Reference 14: http://www.xbrl.org/2003/role/disclosureRef
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+ Details

Prepaid Expenses and Other Current Assets

12 Months Ended

Dec. 31, 2024

Text Block [Abstract]

Prepaid Expenses and Other Current Assets

(6)

Prepaid Expenses and Other Current Assets

Prepaid expenses and other current assets consist of the following (in thousands):


	December 31,		December 31,
	2024		2023
Prepaid insurance	$	517	$	691
Prepaid research and development		128		788
Other prepaid expenses		110		536
Other current assets		75		146
Total prepaid expenses and other current assets	$	830	$	2,161

Prepaid Expenses and Other Current Assets (Detail) - USD ($) $ in Thousands	Dec. 31, 2024	Dec. 31, 2023
Deferred Costs, Capitalized, Prepaid, and Other Assets Disclosure [Abstract]
Prepaid insurance	$ 517	$ 691
Prepaid research and development	128	788
Other prepaid expenses	110	536
Other current assets	75	146
Total prepaid expenses and other current assets	$ 830	$ 2,161

Segment Information - Summary of Research and Development, General and Administrative Expenses, and Restructuring Charges are Significant Segment Expenses (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2024	Dec. 31, 2023
Segment Reporting Information [Line Items]
Total research and development expense	$ 9,154	$ 43,971
Total general and administrative expense	6,631	14,561
Restructuring charge	25,173	0
Facility and all other costs
Segment Reporting Information [Line Items]
Total research and development expense	3,116	11,422
Total general and administrative expense	854	1,172
Restructuring charge	15,497	0
Compensation and benefits
Segment Reporting Information [Line Items]
Total research and development expense	1,979	13,200
Total general and administrative expense	1,964	7,637
Restructuring charge	8,629	0
Consulting and professional services
Segment Reporting Information [Line Items]
Total general and administrative expense	3,813	5,752
Restructuring charge	725	0
Clinical research and external costs
Segment Reporting Information [Line Items]
Total research and development expense	4,059	19,349
Restructuring charge	$ 322	$ 0

Assets Held for Sale, Property and Equipment - Summary of Property and Equipment, Net (Detail) - USD ($) $ in Thousands	Dec. 31, 2024	Dec. 31, 2023
Property Plant And Equipment [Line Items]
Property and equipment, gross		$ 19,887
Less accumulated depreciation		(14,284)
Property and equipment, net	$ 0	5,603
Laboratory Equipment
Property Plant And Equipment [Line Items]
Property and equipment, gross		8,582
Computer and Office Equipment
Property Plant And Equipment [Line Items]
Property and equipment, gross		793
Furniture and Fixtures
Property Plant And Equipment [Line Items]
Property and equipment, gross		500
Leasehold Improvements
Property Plant And Equipment [Line Items]
Property and equipment, gross		9,820
Construction in Progress
Property Plant And Equipment [Line Items]
Property and equipment, gross		$ 192

Assets Held for Sale, Property and Equipment

12 Months Ended

Dec. 31, 2024

Property, Plant and Equipment Assets Held-for-Sale Disclosure [Abstract]

Assets Held for Sale, Property and Equipment

(5)

Assets Held for Sale, Property and Equipment

As of December 31, 2024, assets held for sale are summarized as follows (in thousands):


	December 31,
	2024
Laboratory equipment	$	86
Assets held for sale	$	86

In February 2024, the Company committed to a plan to sell its remaining lab equipment and therefore has classified the amount as assets held for sale on the consolidated balance sheet as of December 31, 2024. The assets held for sale were reported at the lower of the carrying amount or fair value, less costs to sell. During the year ended December 31, 2024, there were impairment charges of $0.8 million incurred related to the lab equipment classified as assets held for sale, which was included in restructuring and other charges. During the second quarter of 2024, the Company engaged a third party to assist with an ongoing auction of its assets held for

sale, which resulted in proceeds of $1.3 million and a $1.2 million gain on disposal of lab equipment during the year ended December 31, 2024.

As of December 31, 2023, property and equipment are summarized as follows (in thousands):


	December 31,
	2023
Laboratory equipment	$	8,582
Computer and office equipment		793
Furniture and fixtures		500
Leasehold improvements		9,820
Construction in progress		192
		19,887
Less accumulated depreciation		(14,284	)
Property and equipment, net	$	5,603

Depreciation expense on property and equipment was $0.3 million and $2.0 million in 2024 and 2023, respectively

Equity-based Compensation and Equity Incentive Plans - Schedule of Equity-based Compensation Expenses by Award Type (Detail) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2024	Dec. 31, 2023
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Equity-based compensation expense	$ 3,169	$ 2,806
Employee Stock
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Equity-based compensation expense	(22)	90
Employee Stock Option
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Equity-based compensation expense	2,064	2,354
Restricted Stock Awards
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Equity-based compensation expense	$ 1,127	$ 362

Related-Party Transactions

12 Months Ended

Dec. 31, 2024

Related-Party Transactions

In June 2019, the Company expanded its collaboration and entered into an agreement with Ginkgo for the research and development of engineered microbial therapeutic products. As of December 31, 2024, Ginkgo owns 422,718 shares of the Company’s outstanding common stock. See Note 11, Collaboration Agreements: Ginkgo Collaboration.

Under the agreement the Company made a prepayment to Ginkgo of $30.0 million for its foundry services that will be provided to the Company over an initial term of five years. Upon the expiration of such initial term and, if applicable, an additional term, any portion of the prepayment that has not been used to purchase services from Ginkgo will be retained by Ginkgo. In February 2024, the Company and its board of directors decided to discontinue the Synpheny-3 trial, significantly reduce its workforce and to evaluate strategic options for the Company. As a result of this decision, the Company would no longer be purchasing services from Ginkgo. During the year ended December 31, 2024, the remaining $5.2 million of prepaid expenses related to this collaboration that were historically recorded in prepaid expenses and other current assets and prepaid research and development, net of current portion on the consolidated balance sheet, were recorded as restructuring and other charges on the consolidated statements of operations and comprehensive loss.

- Definition

The entire disclosure for related party transactions. Examples of related party transactions include transactions between (a) a parent company and its subsidiary; (b) subsidiaries of a common parent; (c) and entity and its principal owners; and (d) affiliates.

+ References

Reference 1: http://www.xbrl.org/2003/role/disclosureRef
-Topic 946
-SubTopic 20
-Name Accounting Standards Codification
-Section 50
-Paragraph 2
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147480990/946-20-50-2

Reference 2: http://www.xbrl.org/2003/role/disclosureRef
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-URI https://asc.fasb.org/1943274/2147480990/946-20-50-5

Reference 3: http://www.xbrl.org/2003/role/disclosureRef
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-URI https://asc.fasb.org/1943274/2147480990/946-20-50-6

Reference 4: http://www.xbrl.org/2003/role/disclosureRef
-Topic 946
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-Subparagraph (c)
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-URI https://asc.fasb.org/1943274/2147477968/946-235-50-2

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-Subparagraph (e)
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-Paragraph 1
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+ Details

Segment Information (Additional Information) (Details)	12 Months Ended
Segment Information (Additional Information) (Details)	Dec. 31, 2024 Segment
Segment Reporting [Abstract]
Number of operating segment	1

Net Loss per Share - Schedule of Computation of Basic and Diluted Net Loss per Share (Detail) - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2024	Dec. 31, 2023
Numerator:
Net Income (Loss)	$ (23,359)	$ (61,273)
Denominator:
Weighted-average common shares outstanding - basic	12,196,209	6,502,279
Weighted-average common shares outstanding - diluted	12,196,209	6,502,279
Net loss per share - basic	$ (1.92)	$ (9.42)
Net loss per share - diluted	$ (1.92)	$ (9.42)

- Definition

The amount of net income (loss) for the period per each share of common stock or unit outstanding during the reporting period.

+ References

+ Details

- Definition

The amount of net income (loss) for the period available to each share of common stock or common unit outstanding during the reporting period and to each share or unit that would have been outstanding assuming the issuance of common shares or units for all dilutive potential common shares or units outstanding during the reporting period.

+ References

+ Details

- Definition

The portion of profit or loss for the period, net of income taxes, which is attributable to the parent.

+ References

+ Details

Segment Information

12 Months Ended

Dec. 31, 2024

Segment Reporting [Abstract]

Segment Information

The CODM manages and allocates resources to the operations of the Company on a total company basis by assessing the overall level of resources available and how to best deploy these resources across functions and research and development projects that are in line with long-term company-wide strategic goals. In making these decisions, the PEO uses consolidated financial information for purposes of evaluating performance, forecasting future period financial results, allocating resources and setting incentive targets. The CODM performs this assessment based on the Company's consolidated net income (loss) that is reported on the consolidated statements of operations and comprehensive loss. Through this analysis, the CODM assesses performance by comparing actual consolidated net income (loss) versus the budget, and then decides how to allocate resources to invest in the Company's research and development programs. The measure of segment assets is reported on the consolidated balance sheets as total assets. In addition, research and development, general and administrative expenses, and restructuring charges are significant segment expenses regularly provided to the PEO with the following categories:

Research and Development


	Years Ended December 31,
	(in thousands)
	2024		2023
Clinical research and external costs	$	4,059	$	19,349
Facility and all other costs		3,116		11,422
Compensation and benefits		1,979		13,200
Total research and development expense	$	9,154	$	43,971

General and Administrative


	Years Ended December 31,
	(in thousands)
	2024		2023
Consulting and professional services	$	3,813	$	5,752
Compensation and benefits		1,964		7,637
Facility and all other costs		854		1,172
Total general and administrative expense	$	6,631	$	14,561

Restructuring Charges


	Years Ended December 31,
	(in thousands)
	2024		2023
Facility and all other costs	$	15,497	$	—
Compensation and benefits		8,629		—
Consulting and professional services		725		—
Clinical research and external costs		322		—
Total restructuring charges	$	25,173	$	—

- Definition

The entire disclosure for reporting segments including data and tables. Reportable segments include those that meet any of the following quantitative thresholds a) it's reported revenue, including sales to external customers and intersegment sales or transfers is 10 percent or more of the combined revenue, internal and external, of all operating segments b) the absolute amount of its reported profit or loss is 10 percent or more of the greater, in absolute amount of 1) the combined reported profit of all operating segments that did not report a loss or 2) the combined reported loss of all operating segments that did report a loss c) its assets are 10 percent or more of the combined assets of all operating segments.

+ References

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+ Details

Summary of Significant Accounting Policies - Additional Information (Detail)	12 Months Ended
	Dec. 31, 2024 USD ($) Segment	Dec. 31, 2023 USD ($)
Summary Of Significant Accounting Policies [Line Items]
Cash equivalents maturity	three months or less
Cash equivalents	$ 18,900,000	$ 24,000,000
Transfers of assets and liabilities between Level 1, Level 2, or Level 3	$ 0	0
Lessee, operating lease, existence of option to extend	true
Lessee, operating lease, option to extend	options to extend the lease when it is reasonably certain that option will be exercised
Term of lease	12 months
Revenue, practical expedient, incremental cost of obtaining contract [true/false]	true
Revenue, practical expedient, remaining performance obligation, description	The Company recognizes as an asset the incremental costs of obtaining a contract with a customer if the costs are expected to be recovered. As a practical expedient, the Company recognizes the incremental costs of obtaining a contract as an expense when incurred if the amortization period of the asset that we otherwise would have recognized is one year or less. To date, the Company has not incurred any incremental costs of obtaining a contract with a customer
Description of tax benefit likely to be realized upon settlement	greater than 50%
Number of operating segment \| Segment	1
Letter of Credit
Summary Of Significant Accounting Policies [Line Items]
Cash	$ 50,000.00	$ 1,100,000
Accounting Standards Update 2023-07 [Member]
Summary Of Significant Accounting Policies [Line Items]
Change in accounting principle, accounting standards update, adopted [true false]	true
Change in accounting principle, accounting standards update, immaterial effect [true false]	true

Nature of Business - Additional Information (Detail) - USD ($) $ in Thousands	Dec. 31, 2024	Dec. 31, 2023
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Cash, cash equivalents, and short-term marketable securities	$ 18,900
Restricted cash	50	$ 1,097
Accumulated deficit	$ (441,651)	$ (418,292)

- Definition

Amount of accumulated undistributed earnings (deficit).

+ References + Details

Consolidated Balance Sheets - USD ($) $ in Thousands	Dec. 31, 2024	Dec. 31, 2023
Current assets:
Cash and cash equivalents	$ 18,860	$ 23,960
Short-term marketable securities	0	23,786
Prepaid expenses and other current assets	830	2,161
Assets held for sale	86	0
Total current assets	19,776	49,907
Property and equipment, net	0	5,603
Right of use asset - operating lease	0	12,102
Restricted cash	50	1,097
Prepaid research and development, net of current portion	0	6,825
Other assets	0	16
Total assets	19,826	75,550
Current liabilities:
Accounts payable	164	1,457
Accrued expenses	2,037	3,000
Lease liability - operating lease	0	4,780
Finance lease obligations	0	4
Purchase warrant laibility	4,874	21,047
Total current liabilities	7,075	30,288
Long-term liabilities:
Lease liability - operating lease, net of current portion	0	12,491
Total long-term liabilities	0	12,491
Commitments and contingencies (Note 16)
Stockholders' equity
Common stock, $0.001 par value 250,000,000 shares authorized as of December 31, 2024 and December 31, 2023; 11,975,901 shares issued and 11,696,109 shares outstanding as of December 31, 2024 and 9,465,949 shares issued and 9,186,157 shares outstanding as of December 31, 2023	12	10
Additional paid-in capital	456,908	453,565
Accumulated other comprehensive income	0	6
Accumulated deficit	(441,651)	(418,292)
Treasury stock, at cost (279,792 shares at December 31, 2024 and at December 31, 2023)	(2,518)	(2,518)
Total stockholders' equity	12,751	32,771
Total liabilities and stockholders' equity	$ 19,826	$ 75,550

Restructuring and Other Charges (Additional Information) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2024	Dec. 31, 2023
Restructuring Cost and Reserve [Line Items]
Restructuring charge	$ 25,173	$ 0
Severance and related costs	6,200
Accrued restructuring charges	1,700
Compensation included in restructuring charges	2,400
Existing Lease Obligations	9,600
Impairment related to lease	9,571	0
Impairment losses	5,000
Restricted cash	50	1,097
Gains on equipment sales	1,200
Gain on lease termination	3,271	0
Total termination payment		10,600
Impairment for in-process research and development	5,200
Restructuring Additional Gain	1,200
Former Headquarter [Member]
Restructuring Cost and Reserve [Line Items]
Gain on lease termination	$ 3,200
Letter of Credit
Restructuring Cost and Reserve [Line Items]
Restricted cash		$ 1,000

Leases - Additional Information (Detail)		1 Months Ended	12 Months Ended
Leases - Additional Information (Detail)	Dec. 31, 2018 ft²	Jul. 31, 2017 USD ($) ft²	Dec. 31, 2024 USD ($)	Dec. 31, 2023 USD ($)
Lessee Lease Description [Line Items]
Laboratory and office space to be leased \| ft²		41,346
Operating lease annual rent		$ 1,000,000
Term of lease			12 months
Lessee, operating lease, existence of option to extend			true
Cash paid included in operating cash flows			$ 2,400,000	$ 5,600,000
Leasehold Improvements Payment			6,600,000
Total termination payment				10,600,000
Restricted cash			50,000	1,097,000
Gain on lease termination			3,271,000	0
LeaseholdImprovementsGross			9,500,000
Existing Lease Obligations			9,600,000
Former Headquarter
Lessee Lease Description [Line Items]
Gain on lease termination			3,200,000
Letter of Credit
Lessee Lease Description [Line Items]
Restricted cash				$ 1,000,000
Azzur Group, LLC
Lessee Lease Description [Line Items]
Total termination payment			300,000
Gain on lease termination			0.04
The Binney Street
Lessee Lease Description [Line Items]
Leasehold Improvements Payment			$ 2,900,000
Master Services Agreement \| Azzur Group, LLC
Lessee Lease Description [Line Items]
Access and use of space under agreement \| ft²	1,014
Term of agreement	68 months

Summary of Significant Accounting Policies (Policies)

12 Months Ended

Dec. 31, 2024

Accounting Policies [Abstract]

Basis of Presentation

The accompanying consolidated financial statements have been prepared in accordance with accounting principles generally accepted in the United States (U.S.) (U.S. GAAP or GAAP).

Principles of Consolidation

Use of Estimates

Cash Equivalents

Concentration of Credit Risk

Restricted Cash


	December 31,		December 31,
	2024		2023
Cash and cash equivalents	$	18,860	$	23,960
Restricted cash		50		1,097
Total cash, cash equivalents, and restricted cash shown in the consolidated statement of cash flows	$	18,910	$	25,057

Fair Value

•

Level 1 – Utilize observable inputs such as quoted prices in active markets for identical assets or liabilities;

•

Level 2 – Utilize data points that are either directly or indirectly observable, such as quoted prices, interest rates and yield curves;

•

Level 3 – Utilize unobservable data points in which there is little or no market data, which require the Company to develop its own assumptions for the asset or liability.

Available-for-Sale Securities

Property and Equipment

Depreciation begins at the time the asset is placed in service. Depreciation is provided over the following estimated useful lives:


Asset classification		Useful life
Computer and office equipment		3 years
Furniture and fixtures		5 years
Laboratory equipment		5 years
Leasehold improvements		Lesser of useful life or remaining lease term

Impairment of Long-Lived Assets

Impairment of Long‑Lived Assets

Leases

Research and Development Costs

Warrants

use of professional judgment, is conducted at the time of warrant issuance and as of each subsequent quarterly period end date while the warrants are outstanding.

Revenue recognition

Licenses of Intellectual Property

Research and Development Services

Customer Options

Milestone Payments

Royalties

Contract Costs

Equity-Based Compensation

Equity‑Based Compensation

Treasury stock purchases are accounted for under the cost method whereby the entire cost of the acquired stock is recorded as treasury stock.

Recently Issued and Adopted Accounting Pronouncements

Accrued Expenses

12 Months Ended

Dec. 31, 2024

Payables and Accruals [Abstract]

Accrued Expenses

(7)

Accrued Expenses

Accrued expenses consist of the following (in thousands):


	December 31,		December 31,
	2024		2023
Payroll related	$	126	$	2,556
Professional fees		205		290
Research and development		—		91
Restructuring costs		1,656		—
Other		50		63
Total accrued expenses	$	2,037	$	3,000

Fair Value of Financial Instruments

12 Months Ended

Dec. 31, 2024

Fair Value Disclosures [Abstract]

Fair Value of Financial Instruments

(3)

Fair Value of Financial Instruments

The tables below present information about the Company’s assets and liabilities that are measured at fair value on a recurring basis as of December 31, 2024 and 2023 and indicate the fair value hierarchy of the valuation techniques the Company utilized to determine such fair value, as described under Note 2, Summary of Significant Accounting Policies.

The Company’s investment portfolio includes many fixed income securities that do not always trade on a daily basis. As a result, the pricing services used by the Company applied other available information as applicable through processes such as benchmark yields, benchmarking of like securities, sector groupings and matrix pricing to prepare evaluations. In addition, model processes were used to assess interest rate impact and develop prepayment scenarios. These models take into consideration relevant credit information, perceived market movements, sector news and economic events. The inputs into these models may include benchmark yields, reported trades, broker-dealer quotes, issuer spreads and other relevant data.

The Company accounts for issued warrants either as derivative liabilities or as equity instruments depending on the specific terms of the agreement. Warrants that are equity-classified instruments and recorded in additional paid-in capital at issuance are not subject to remeasurement. The purchase warrants issued in October 2023 are liability classified and recorded at fair value using the Black-Scholes option-pricing model at issuance, with any subsequent changes in fair value recognized in the consolidated statements of operations. We periodically evaluate changes in facts and circumstances that could impact the classification of warrants. None of the purchase warrants have been exercised since their issuance.

At December 31, 2024 and 2023, the Company has classified assets and liabilities measured at fair value on a recurring basis as follows (in thousands):


	Fair Value Measurements at Reporting Date Using
	December 31,		Quoted Prices in Active Markets for Identical Assets		Significant Other Observable Inputs		Significant Unobservable Inputs
Description	2024		(Level 1)		(Level 2)		(Level 3)
Assets:
Money market funds	$	18,860	$	18,860	$	—	$	—
Total	$	18,860	$	18,860	$	—	$	—
Liabilities:
Purchase warrant liability	$	4,874	$	—	$	—	$	4,874
Total	$	4,874	$	—	$	—	$	4,874

	Fair Value Measurements at Reporting Date Using
	December 31,		Quoted Prices in Active Markets for Identical Assets		Significant Other Observable Inputs		Significant Unobservable Inputs
Description	2023		(Level 1)		(Level 2)		(Level 3)
Assets:
Money market funds	$	15,476	$	15,476	$	—	$	—
Commercial paper (included in cash and cash equivalents)		8,484		—		8,484		—
Commercial paper		14,342		—		14,342		—
U.S. government agency securities and treasuries		9,444		6,956		2,488		—
Total	$	47,746	$	22,432	$	25,314	$	—
Liabilities:
Purchase warrant liability	$	21,047	$	—	$	—	$	21,047
Total	$	21,047	$	—	$	—	$	21,047

Cash equivalents, prepaid expenses and other current assets, accounts payable and accrued expenses at December 31, 2024 and December 31, 2023 are carried at amounts that approximate fair value due to their short-term maturities. Finance lease obligations at December 31, 2023 approximate fair value as they bear interest at a rate approximating a market interest rate.


December 31, 2024	Amortized Cost		Gross unrealized gains		Gross unrealized losses		Fair Value
Money market funds (included in cash and cash equivalents)	$	18,860	$	—	$	—	$	18,860
Total	$	18,860	$	—	$	—	$	18,860

December 31, 2023	Amortized Cost		Gross unrealized gains		Gross unrealized losses		Fair Value
Money market funds (included in cash and cash equivalents)	$	15,476	$	—	$	—	$	15,476
Commercial paper (included in cash and cash equivalents)		8,482		2		—		8,484
Total	$	23,958	$	2	$	—	$	23,960

Assumptions Used in Determining Fair Value of Warrants

The assumptions used in the Black-Scholes option-pricing model for the purchase warrants on the consolidated balance sheets at December 31, 2024 and December 31, 2023 are included below:


	December 31, 2024			December 31, 2023
Expected Term	3.75 years			4.75 years
Weighted-average, risk free interest rate		4.3	%		3.9	%
Expected volatility		90.0	%		94.0	%
Dividend yield		—			—
Strike price	$	3.41		$	3.41
Stock price	$	1.40		$	3.85

- Definition

The entire disclosure for the fair value of financial instruments (as defined), including financial assets and financial liabilities (collectively, as defined), and the measurements of those instruments as well as disclosures related to the fair value of non-financial assets and liabilities. Such disclosures about the financial instruments, assets, and liabilities would include: (1) the fair value of the required items together with their carrying amounts (as appropriate); (2) for items for which it is not practicable to estimate fair value, disclosure would include: (a) information pertinent to estimating fair value (including, carrying amount, effective interest rate, and maturity, and (b) the reasons why it is not practicable to estimate fair value; (3) significant concentrations of credit risk including: (a) information about the activity, region, or economic characteristics identifying a concentration, (b) the maximum amount of loss the entity is exposed to based on the gross fair value of the related item, (c) policy for requiring collateral or other security and information as to accessing such collateral or security, and (d) the nature and brief description of such collateral or security; (4) quantitative information about market risks and how such risks are managed; (5) for items measured on both a recurring and nonrecurring basis information regarding the inputs used to develop the fair value measurement; and (6) for items presented in the financial statement for which fair value measurement is elected: (a) information necessary to understand the reasons for the election, (b) discussion of the effect of fair value changes on earnings, (c) a description of [similar groups] items for which the election is made and the relation thereof to the balance sheet, the aggregate carrying value of items included in the balance sheet that are not eligible for the election; (7) all other required (as defined) and desired information.

+ References

Reference 1: http://www.xbrl.org/2003/role/exampleRef
-Topic 820
-SubTopic 10
-Name Accounting Standards Codification
-Section 55
-Paragraph 107
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147482078/820-10-55-107

Reference 2: http://www.xbrl.org/2003/role/exampleRef
-Topic 820
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-Name Accounting Standards Codification
-Section 55
-Paragraph 100
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147482078/820-10-55-100

Reference 3: http://www.xbrl.org/2003/role/disclosureRef
-Topic 820
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 2
-Subparagraph (c)(3)
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147482106/820-10-50-2

Reference 4: http://www.xbrl.org/2003/role/disclosureRef
-Topic 820
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-Name Accounting Standards Codification
-Section 50
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-Subparagraph (a)
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-URI https://asc.fasb.org/1943274/2147482106/820-10-50-6A

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-Name Accounting Standards Codification
-Section 50
-Paragraph 2E
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147482106/820-10-50-2E

Reference 6: http://www.xbrl.org/2003/role/disclosureRef
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-Topic 820
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-Name Accounting Standards Codification
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-Section 50
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-Subparagraph (e)
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Reference 9: http://www.xbrl.org/2003/role/disclosureRef
-Topic 820
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-Name Accounting Standards Codification
-Section 50
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-Subparagraph (d)
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147482106/820-10-50-6A

Reference 10: http://www.xbrl.org/2003/role/disclosureRef
-Topic 820
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-Name Accounting Standards Codification
-Section 50
-Paragraph 2
-Subparagraph (h)
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147482106/820-10-50-2

Reference 11: http://www.xbrl.org/2003/role/disclosureRef
-Topic 820
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 2
-Subparagraph (g)
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147482106/820-10-50-2

Reference 12: http://www.xbrl.org/2003/role/disclosureRef
-Topic 940
-SubTopic 820
-Name Accounting Standards Codification
-Section 50
-Paragraph 1
-Subparagraph (a)
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147478119/940-820-50-1

+ Details

Leases

12 Months Ended

Dec. 31, 2024

Leases [Abstract]

Leases

Operating Leases

301 Binney Street

In July 2017, the Company entered into an agreement to lease approximately 41,346 square feet of laboratory and office space at 301 Binney Street in Cambridge, Massachusetts, or the Binney Street Lease. In conjunction with the lease, the Company established a letter of credit of approximately $1.0 million secured by cash balances included in restricted cash.

On June 26, 2024 (the “Termination Date”), the Company entered into a Lease Termination Agreement (the “Termination Agreement”) for its corporate headquarters in Cambridge, Massachusetts, with the landlord which, effective immediately, terminated the lease. In exchange for the early termination of the lease pursuant to the Termination Agreement, the Company made a total termination payment of $10.6 million, of which $1.0 million was from a letter of credit associated with the lease and classified in the consolidated balance sheets as noncurrent restricted cash at December 31, 2023. As a result of the lease termination, the Company recorded a gain on lease termination, associated with its former headquarters, of $3.2 million, for the year ended December 31, 2024.

The Binney Street Lease included $9.5 million of leasehold improvements, of which $2.9 million was paid by the Company and $6.6 million was landlord-funded. The Company capitalized the leasehold improvements which were included in property and

equipment, net on the consolidated balance sheets and were amortized on a straight-line basis over the remaining lease term. The leasehold improvements were subsequently fully impaired in the first quarter of 2024.

Azzur Suite

During the year ended December 31, 2018, the Company entered into an agreement with Azzur Group, LLC (Azzur) whereby Azzur agreed to provide the Company with access to, and the use of, cleanroom space in Waltham, Massachusetts, or the Azzur Suite Lease. The Azzur Suite Lease was subsequently amended in April 2021, January 2022, November 2022 and December 2023. The Azzur Suite Lease, as amended, provided an initial rental term of 68 months, and a rental area of approximately 1,014 square feet.

In connection with the corporate restructuring, the Company executed the option for early termination of the Azzur Suite Lease via written notice to Azzur and as a result the lease was terminated effective April 8, 2024. In exchange for the early termination of the lease, the Company made a total termination payment of $0.3 million which is included in restructuring and other charges on the consolidated statements of operations and other comprehensive loss. The Company also recorded a gain on lease termination, associated with the termination of the Azzur Suite Lease, of $0.04 million, for the year ended December 31, 2024.

Leases classified as operating leases are included in operating lease ROU assets, current operating lease liabilities and noncurrent operating lease liabilities in our consolidated balance sheets. The operating lease right-of-use asset and operating lease liability represents the Binney Street Lease and the Azzur Suite Lease. Cash paid for amounts included in the present value of operating lease liabilities was $2.4 million and $5.6 million during the years ended December 31, 2024 and 2023, respectively, which is included in operating cash flows, all of which were incurred prior to the lease termination.

The components of lease cost for operating leases for the years ended December 31, 2024 and 2023 were (in thousands):


	For the years ended December 31,
Operating leases	2024		2023
Operating lease cost	$	1,582	$	4,869
Variable lease cost		1,091		1,583
Total lease cost	$	2,673	$	6,452

The right-of-use asset for the operating lease is disclosed on the consolidated balance sheets.

The lease cost for finance leases during the years ended December 31, 2024 and 2023, and the finance lease liability at December 31, 2024 and December 31, 2023, were not material.

Accrued Expenses (Tables)

12 Months Ended

Dec. 31, 2024

Payables and Accruals [Abstract]

Schedule of Accrued Expenses

Accrued expenses consist of the following (in thousands):


	December 31,		December 31,
	2024		2023
Payroll related	$	126	$	2,556
Professional fees		205		290
Research and development		—		91
Restructuring costs		1,656		—
Other		50		63
Total accrued expenses	$	2,037	$	3,000

Equity-based Compensation and Equity Incentive Plans - Schedule of Stock Option Activity Under 2015 and 2017 Plan (Detail) - 2015 and 2017 Plan - USD ($)
$ / shares in Units, $ in Thousands

12 Months Ended

Dec. 31, 2024

Dec. 31, 2023

Share-based Compensation Arrangement by Share-based Payment Award [Line Items]

Outstanding Beginning balance, Number of options

612,761

Granted, Number of options

44,701

Exercised, Number of options

(82,293)

Cancelled/Forfeited, Number of options

(250,186)

Outstanding Ending balance, Number of options

324,983

612,761

Number of options, Vested or expected to vest

324,983

Number of options, Exercisable

231,360

Beginning balance, Weighted-average price

$ 9.13

Granted, Weighted-average price

4.2

Exercised, Weighted-average price

1.85

Cancelled/Forfeited, Weighted-average price

7.08

Ending balance, Weighted-average price

11.88

$ 9.13

Weighted-average price Vested or expected to vest

11.88

Weighted-average price, Exercisable

$ 15.94

Outstanding, weighted average remaining contractual term (Year)

7 years

7 years 9 months 18 days

Weighted average remaining contractual term, Vested or expected to vest

7 years

Weighted average remaining contractual term, Exercisable

6 years 8 months 12 days

Beginning balance, Aggregate Intrinsic value

^[1]

$ 1,026

Granted, Aggregate Intrinsic value

^[1]

Exercised, Aggregate Intrinsic value

^[1]

Cancelled/Forfeited, Aggregate Intrinsic value

^[1]

Ending balance, Aggregate Intrinsic value

^[1]

$ 1,026

Aggregate Intrinsic value, Vested or expected to vest at December 31, 2024

^[1]

Aggregate Intrinsic value, Exercisable at December 31, 2024

^[1]

$ 0

[1]

Accrued Expenses - Schedule of Accrued Expenses (Detail) - USD ($) $ in Thousands	Dec. 31, 2024	Dec. 31, 2023
Payables and Accruals [Abstract]
Payroll related	$ 126	$ 2,556
Professional fees	205	290
Research and development	0	91
Restructuring costs	1,656	0
Other	50	63
Total accrued expenses	$ 2,037	$ 3,000

Assets Held for Sale, Property and Equipment (Tables)

12 Months Ended

Dec. 31, 2024

Property, Plant and Equipment Assets Held-for-Sale Disclosure [Abstract]

Schedule of Assets Held for Sale

As of December 31, 2024, assets held for sale are summarized as follows (in thousands):


	December 31,
	2024
Laboratory equipment	$	86
Assets held for sale	$	86

Schedule of Property and Equipment, Net

As of December 31, 2023, property and equipment are summarized as follows (in thousands):


	December 31,
	2023
Laboratory equipment	$	8,582
Computer and office equipment		793
Furniture and fixtures		500
Leasehold improvements		9,820
Construction in progress		192
		19,887
Less accumulated depreciation		(14,284	)
Property and equipment, net	$	5,603

Related-Party Transactions - Additional Information (Detail) - USD ($) $ in Millions	1 Months Ended
	Jun. 30, 2019	Dec. 31, 2024	Dec. 31, 2023	Nov. 09, 2023
Related Party Transaction [Line Items]
Common stock, outstanding		11,696,109	9,186,157	539,685
Ginkgo Bioworks, Inc.
Related Party Transaction [Line Items]
Common stock, outstanding		422,718
Prepayment to related party for collaboration agreement	$ 30.0
Related party transaction collaboration agreement, initial term	5 years
Current pre-paid research and development		$ 5.2
Common Stock \| Ginkgo Bioworks, Inc.
Related Party Transaction [Line Items]
Sale of common stock, shares	422,718

Nature of Business

12 Months Ended

Dec. 31, 2024

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Nature of Business

(1)

Nature of Business

Organization

Synlogic, Inc., together with its wholly owned and consolidated subsidiaries (Synlogic or the Company), is a biopharmaceutical company applying synthetic biology to the discovery and development of Synthetic Biotics. Synthetic Biotics are generated from Synlogic’s proprietary platform, leveraging a reproducible, modular approach to the generation of novel drug candidates that perform or deliver critical therapeutic functions. Synthetic Biotics are designed to metabolize a toxic substance, compensate for missing or damaged metabolic pathways or deliver combinations of therapeutic factors. Synlogic’s goal is to discover, develop and ultimately commercialize Synthetic Biotics. Since incorporation, the Company has devoted substantially all of its efforts to the research and development of its product candidates.

In February 2024, the Company and its board of directors decided to discontinue the Synpheny-3 trial and to conduct a comprehensive review of strategic alternatives. The Company also announced a corporate restructuring that resulted in a reduction in its workforce, leaving one remaining full-time employee, in addition to consultants, to, among other things, support the strategic review process and current business operations. (see Note 8, Restructuring and Other Charges).

Going Concern and Liquidity

The Company’s consolidated financial statements have been prepared assuming it will continue as a going concern. The going concern assumption contemplates the continuity of operations, and the realization of assets and the satisfaction of liabilities in the ordinary course of business. The Company has historically generated negative cash flows from operations and has an accumulated deficit of $441.7 million at December 31, 2024. At December 31, 2024, the Company had $18.9 million in unrestricted cash and cash equivalents. Following the execution of the corporate restructuring over the course of the year ended December 31, 2024 (see Note 8, Restructuring and Other Charges), the Company has determined its current cash and cash equivalents as of December 31, 2024 will be sufficient to fund its operations at the current levels for at least the next 12 months from the date of this filing. The Company expects ongoing expenses to decrease due to the decision to discontinue the Synpheny-3 clinical trial and conduct workforce reductions however, as the Company continues to review strategic alternatives, the Company will continue to incur costs and expenditures in connection with the process of evaluating strategic alternatives.

Risks and Uncertainties

As an early-stage company, the Company is subject to a number of risks common to other life science companies, including, but not limited to, raising additional capital, development by its competitors of new technological innovations, risk of failure in preclinical and clinical studies, safety and efficacy of its product candidates in clinical trials, the risk of relying on external parties such as contract research organizations (CROs) and contract manufacturing organizations (CMOs), the regulatory approval process, market acceptance of the Company’s products once approved, lack of marketing and sales history, dependence on key personnel and protection of proprietary technology. The Company’s therapeutic programs are currently pre-commercial, spanning discovery through early development and will require significant additional research and development efforts, including extensive preclinical and clinical testing and regulatory approval, prior to commercialization of any product candidates. These efforts require significant amounts of additional capital, adequate personnel, infrastructure, and extensive compliance-reporting capabilities. There can be no assurance that the Company’s research and development will be successfully completed, that adequate protection for the Company’s intellectual property will be obtained, that any products developed will obtain necessary regulatory approval or that any approved products will be commercially viable. Even if the Company’s product development efforts are successful, it is uncertain when, if ever, the Company will generate revenue from product sales. The Company may never achieve profitability, and unless and until it does, it will continue to need to raise additional capital or obtain financing from other sources, such as strategic collaborations or alliances.

Consolidated Statements of Operations and Comprehensive Loss - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2024	Dec. 31, 2023
Income Statement [Abstract]
Revenue	$ 8	$ 3,371
Operating expenses:
Research and development	9,154	43,971
General and administrative	6,631	14,561
Restructuring and other charges	25,173	0
Total operating expenses	40,958	58,532
Loss from operations	(40,950)	(55,161)
Other income (expense):
Interest and investment income	1,425	2,469
Interest expense	0	(1)
Change in fair value of purchase warrant liability	16,173	(7,652)
Other expense	(2)	(914)
Total other income (expense), net	17,596	(6,098)
Loss before income taxes	(23,354)	(61,259)
Income tax expense	(5)	(14)
Net loss	$ (23,359)	$ (61,273)
Net loss per share - basic and diluted	$ (1.92)	$ (9.42)
Net loss per share - basic and diluted	$ (1.92)	$ (9.42)
Weighted-average common stock outstanding - basic and diluted	12,196,209	6,502,279
Weighted-average common stock outstanding - basic and diluted	12,196,209	6,502,279
Comprehensive income (loss):
Net Income (Loss)	$ (23,359)	$ (61,273)
Net unrealized (loss) gain on marketable securities	(6)	167
Comprehensive loss	$ (23,365)	$ (61,106)

Segment Information (Tables)

12 Months Ended

Dec. 31, 2024

Segment Reporting [Abstract]

Schedule of Research and Development, General and Administrative Expenses, and Restructuring Charges are Significant Segment Expenses

In addition, research and development, general and administrative expenses, and restructuring charges are significant segment expenses regularly provided to the PEO with the following categories:

Research and Development


	Years Ended December 31,
	(in thousands)
	2024		2023
Clinical research and external costs	$	4,059	$	19,349
Facility and all other costs		3,116		11,422
Compensation and benefits		1,979		13,200
Total research and development expense	$	9,154	$	43,971

General and Administrative


	Years Ended December 31,
	(in thousands)
	2024		2023
Consulting and professional services	$	3,813	$	5,752
Compensation and benefits		1,964		7,637
Facility and all other costs		854		1,172
Total general and administrative expense	$	6,631	$	14,561

Restructuring Charges


	Years Ended December 31,
	(in thousands)
	2024		2023
Facility and all other costs	$	15,497	$	—
Compensation and benefits		8,629		—
Consulting and professional services		725		—
Clinical research and external costs		322		—
Total restructuring charges	$	25,173	$	—

Income Taxes (Tables)

12 Months Ended

Dec. 31, 2024

Income Tax Disclosure [Abstract]

Schedule of Temporary Differences Between Basis of Deferred Tax Assets and Liabilities


	December 31,
	2024			2023
Deferred tax assets:
Net operating loss carryforwards	$	102,145		$	87,396
Tax credit carryforwards		10,931			10,401
Accrued expenses		132			84
Property and equipment		28			1,113
Lease liabilities		—			4,718
Equity compensation		2,191			3,270
Amortizable intangibles		984			1,100
Amortizable research expenditures (1)		17,958			20,202
Other		64			77
Gross deferred tax assets		134,433			128,361
Deferred tax liabilities:
Right of use assets		—			(3,306	)
Gross deferred tax liabilities		—			(3,306	)
Valuation allowance		(134,433	)		(125,055	)
Net deferred tax assets	$	—		$	—

Reconciliation of Statutory Federal Income Tax Rate to Company's Effective Income Tax Rate

A reconciliation of the statutory federal income tax rate to the Company’s effective income tax rate is as follows:


	Years ended December 31,
	2024			2023
	Tax Rate			Tax Rate
U.S. federal statutory rate		21	%		21	%
State income taxes, net of federal benefit		9	%		6	%
Other permanent differences		9	%		(3	)%
Tax credits		2	%		2	%
Other items		(1	)%		(1	)%
Net change in valuation allowance		(40	)%		(25	)%
Effective income tax rate		—			—

Schedule of Valuation Allowance

A roll-forward of the valuation allowance for the years ended December 31, 2024 and 2023 is as follows (in thousands):


	Years ended December 31,
	2024			2023
Balance at beginning of year	$	(125,055	)	$	(109,599	)
Increase in valuation allowance		(9,378	)		(15,456	)
Balance at end of year	$	(134,433	)	$	(125,055	)

Available-for-Sale Securities - Summary of Available-for-Sale Securities Held (Detail) $ in Thousands	Dec. 31, 2023 USD ($)
Schedule of Available-for-sale Securities [Line Items]
Amortized cost	$ 23,782
Gross unrealized gains	5
Gross unrealized losses	(1)
Fair Value	23,786
U.S. Treasuries
Schedule of Available-for-sale Securities [Line Items]
Amortized cost	9,444
Gross unrealized gains	1
Gross unrealized losses	(1)
Fair Value	9,444
Commercial Paper
Schedule of Available-for-sale Securities [Line Items]
Amortized cost	14,338
Gross unrealized gains	4
Gross unrealized losses	0
Fair Value	$ 14,342

- Definition

Amount of investment in debt security measured at fair value with change in fair value recognized in other comprehensive income (available-for-sale).

+ References

Reference 1: http://www.xbrl.org/2003/role/exampleRef
-Topic 820
-SubTopic 10
-Name Accounting Standards Codification
-Section 55
-Paragraph 103
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+ Details

- Definition

Line items represent financial concepts included in a table. These concepts are used to disclose reportable information associated with domain members defined in one or many axes to the table.

+ References

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-Subparagraph (a)
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147481800/320-10-50-3

Reference 10: http://www.xbrl.org/2003/role/disclosureRef
-Topic 320
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 3
-Subparagraph (b)
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147481800/320-10-50-3

Reference 11: http://www.xbrl.org/2003/role/disclosureRef
-Topic 320
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 3
-Subparagraph (c)
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147481800/320-10-50-3

Reference 12: http://www.xbrl.org/2003/role/disclosureRef
-Topic 320
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 3
-Subparagraph (d)
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147481800/320-10-50-3

+ Details

Equity-based Compensation and Equity Incentive Plans (Tables)

12 Months Ended

Dec. 31, 2024

Schedule of Restricted Common Stock Activity

The following table shows restricted common stock activity:


	Restricted stock awards
				Weighted average grant date
	Number of			fair value
	shares			(per share)
Unvested at December 31, 2023		36,046		$	25.24
Granted		362,700			4.44
Vested		(10,800	)		25.96
Forfeited		(193,880	)		5.58
Unvested at December 31, 2024		194,066		$	5.97

Schedule of Equity-based Compensation Expenses


	Years Ended December 31,
	2024		2023
Research and development	$	232	$	1,024
General and administrative		570		1,782
Restructuring charges: expense acceleration		2,367		—
	$	3,169	$	2,806

Schedule of Equity-based Compensation Expenses by Award Type

The following table summarizes equity‑based compensation expense by type of award for the years ended December 31, 2024 and 2023 (in thousands):


	Years Ended December 31,
	2024			2023
Stock options	$	2,064		$	2,354
Restricted stock awards		1,127			362
ESPP		(22	)		90
	$	3,169		$	2,806

2015 and 2017 Plan

Schedule of Weighted Average Assumption Used Black-Scholes Option-pricing Model for Stock Options Issued to Employees and Non-employees


	Years Ended December 31,
Employees:	2024	2023
Expected term	5.6 years	6.2 years
Weighted-average, risk-free interest rate	3.9%	3.7%
Expected volatility	92.0%	82.4%
Dividend yield	—	—

Schedule of Stock Option Activity

The following table summarizes stock option activity under the 2015 and 2017 Plans.


	Stock options outstanding
						Weighted
						average
				Weighted		remaining		Aggregate
				average		contractual		intrinsic
	Number of			exercise		term		value (a)
	options			price		(in years)		(in thousands)
Outstanding at December 31, 2023		612,761		$	9.13		7.8	$	1,026
Granted		44,701			4.20				—
Exercised		(82,293	)		1.85				5
Cancelled/Forfeited		(250,186	)		7.08				—
Outstanding at December 31, 2024		324,983			11.88		7.0	$	—

Vested or expected to vest at December 31, 2024		324,983		$	11.88		7.0	$	—
Exercisable at December 31, 2024		231,360		$	15.94		6.7	$	—

Leases - Summary of Maturity of Lease Liabilities for Operating Leases (Detail) - USD ($) $ in Thousands	Dec. 31, 2024	Dec. 31, 2023
Operating Leases
Current lease liabilities	$ 0	$ 4,780
Long-term lease liabilities	$ 0	$ 12,491

Net Loss per Share (Tables)

12 Months Ended

Dec. 31, 2024

Earnings Per Share [Abstract]

Schedule of Computation of Basic and Diluted Net Loss per Share

The following table sets forth the computation of basic and diluted net loss per share (in thousands, except for share and per share amounts):


	Years Ended December 31,
	2024			2023
Numerator:
Net loss	$	(23,359	)	$	(61,273	)
Denominator:
Weighted-average common shares outstanding - basic and diluted		12,196,209			6,502,279
Net loss per share - basic and diluted	$	(1.92	)	$	(9.42	)

Schedule of Potentially Common Shares Excluded from Calculation of Net Loss Per share


	As of December 31,
	2024		2023
Purchase warrants		7,394,363		7,394,363
Unvested restricted common stock awards		194,066		36,046
Outstanding options to purchase common stock		324,983		612,761
Potential shares issuable under the ESPP		—		19,751
		7,913,412		8,062,921

Assets Held for Sale, Property and Equipment - Summary of Assets Held for Sale (Details) $ in Thousands	Dec. 31, 2024 USD ($)
Property, Plant and Equipment [Line Items]
Assets held for sale	$ 86
Laboratory Equipment
Property, Plant and Equipment [Line Items]
Assets held for sale	$ 86